Table 1 List and description of Integrative Genomics Viewer Navigator (IGVNav) calls and tags used to annotate variants in order of appearance on the IGVNav interface with associated supplementary figure number.

Somatic

S

Variant has sufficient support in the tumor with absence of obvious sequencing artifacts

S1

Germline

G

Variant that has sufficient support in the normal sample beyond what is considered attributable to tumor contamination of the normal

S2

Ambiguous

A

Variant does not meet acceptable criteria for any other label

S3

Fail

F

Variant with low variant support and/or reads that indicate sequencing artifacts

S4

Adjacent Indel

AI

Variant is attributable to misalignment caused by a nearby insertion or deletion

S16

Ambiguous Other

AO

Variant is surrounded by inconclusive genomic features that cannot be explained by other tags

S22

Directional

D

Variant is only (or mostly) found on reads in the same direction (positive or negative)

S5

Dinucleotide repeat

DN

Variant is adjacent to a region in the reference genome that has two alternating nucleotides (e.g., TGTGTG…)

S20

End of reads

E

Variant is only seen close to the end (within 30 base pairs) of variant-supporting reads

S18

High Discrepancy Region

HDR

Variant is supported by reads that have other recurrent mismatches across the track and in multiple tracks

S12

Low Count Normal

LCN

Variant has inadequate coverage in the normal track, thus preventing effective comparison with the tumor track

S7

Low Count Tumor

LCT

Variant has inadequate coverage in the tumor track, thus preventing effective comparison with the normal track

S8

Low Mapping quality

LM

Variant is mostly supported by reads that have low mapping quality

S13

Low Variant Frequency

LVF

Variant has low variant allele frequency (VAF) samples

S10

Multiple Mismatches

MM

Variant is supported by reads that have other mismatched base pairs

S11

Mononucleotide repeat

MN

Variant is adjacent to a region in the reference genome that has a single-nucleotide repeat (e.g., AAAAAA…)

S19

Multiple Variants

MV

Variant locus has read support for three or more alleles

S9

No Count Normal

NCN

Variant has no coverage in the normal track, thus preventing effective comparison with the tumor track

S6

Short Inserts

SI

Variant is found mostly on small nucleic acid fragments whereby sequencing from each end results in overlapping reads

S15

Short Inserts Only

SIO

Variant is exclusively found on small nucleic acid fragments such that sequencing from each end results in overlapping reads

S15

Same Start End

SSE

Variant is only observed in reads that start and stop at the same positions

S17

Tumor in Normal

TN

Variant has read support in the normal track

S14

Tandem Repeat

TR

Variant is adjacent to a region in the reference genome that has three or more alternating nucleotides (e.g., GTGGTGGTG…)

S21