Sample Resequencing Stats
Note: The mutation counts shown below represent unfiltered mutation sets.
| ALE, Flask, Isolate |
Predicted Mutations |
Mean Coverage |
Total Reads |
Percent Mapped |
Mapped Reads |
Average Read Length |
|
A1 F3 I153 R1
|
9 |
31.4 |
1878488 |
94.6% |
1777049 |
83.6 |
Breseq alignment
BRESEQ :: Evidence
|
| evidence |
seq id |
position |
mutation |
annotation |
gene |
description |
| RA |
NZ_CP009273 |
4,172,812 |
T→G |
V547G (GTT→GGT) |
rpoB → |
DNA‑directed RNA polymerase subunit beta |
|
| |
seq id |
position |
ref |
new |
freq |
score (cons/poly) |
reads |
annotation |
genes |
product |
| * | NZ_CP009273 | 4,172,812 | 0 | T | G | 94.1%
| 179.0
/ ‑1.0
| 51 | V547G (GTT→GGT) | rpoB | DNA‑directed RNA polymerase subunit beta |
| Reads supporting (aligned to +/- strand): ref base T (2/1); new base G (25/23); total (27/24) |
| Fisher's exact test for biased strand distribution p-value = 1.00e+00 |
| Kolmogorov-Smirnov test that lower quality scores support variant p-value = 9.98e-01 |
CAACCCGCTGTCTGAGATTACGCACAAACGTCGTATCTCCGCACTCGGCCCAGGCGGTCTGACCCGTGAACGTGCAGGCTTCGAAGTTCGAGACGTACACCCGACTCACTACGGTCGCGTATGTCCAATCGAAACCCCTGAAGGTCCGAACATCGGTCTGATCAACTC > NZ_CP009273/4172726‑4172893
|
caacCCGCTGTCTGAGATTACGCACAAACGTCGTATCTCCGCACTCGGCCCAGGCGGTCTGACCCGTGAACGTGCAGGCTTCGAAGGTCg < 1:476748/90‑1 (MQ=255)
acCCGCTGTCTGAGATTACGCACAAACGTCGTATCTCCGCACTCGGCCCAGGCGGTCTGACCCGTGAACGTGCAGGCTTCGAAGTTCgag > 2:823949/1‑90 (MQ=255)
acCCGCTGTCTGAGATTACGCACAAACGTCGTATCTCCGCACTCGGCCCAGGCGGTCTGACCCGTGAACGTGCAGGCTTCGAAGGTCgag > 1:107920/1‑90 (MQ=255)
cTGTCTGAGATTACGCACAAACGTCGTATCTCCGCACTCGGCCCAGGCGGTCTGACCCGTGAACGTGCAGGCTTCGAAGGTCGAGACGTa > 1:199542/1‑90 (MQ=255)
cTGTCTGAGATTACGCACAAACGTCGTATCTCCGCACTCGGCCCAGGCGGTCTGACCCGTGAACGTGCAGGCTTCGAAGGTCGAGACGTa > 2:510070/1‑90 (MQ=255)
cTGTCTGAGATTACGCACAAACGTCGTATCTCCGCACTCGGCCCAGGCGGTCTGACCCGTGAACGTGCAGGCTTCGAAGGTCGAGACGTa > 1:834240/1‑90 (MQ=255)
cTGTCTGAGATTACGCACAAACGTCGTATCTCCGCACTCGGCCCAGGCGGTCTGACCCGTGAACGTGCAGGCTTCGAAGGTCGAGACGTa > 1:345189/1‑90 (MQ=255)
tGAGATTACGCACAAACGTCGTATCTCCGCACTCGGCCCAGGCGGTCTGACCCGTGAACGTGCAGGCTTCGAAGGTCGAGACGTACAccc < 2:160140/90‑1 (MQ=255)
gaTTCCGCCCAAACGTCGTATCTCCGCACTCGGCCCAGGCGGTCTGACCCGTGAACGTGCAGGCTTCGAAGGTCGAGACGTACACCCGAc < 2:717689/90‑1 (MQ=255)
gaTTACGCACAAACGTCGTATCTCCGCACTCGGCCCAGGCGGTCTGACCCGTGAACGTGCAGGCTTCGAAGGTCGAGACGTACACCCGAc < 1:178164/90‑1 (MQ=255)
ccGCACAAACGTCGTATCTGGGTACTCGGTCCGGGCGGCTTACCCCGGGAAAAGGCAGCCTGCGAAGTTTGAGACGTACTCCCAACTCag > 1:752916/2‑89 (MQ=255)
aCGCACAAACGTCGTATCTCCGCACTCGGCCCAGGCGGTCTGACCCGTGAACGTGCAGGCTTCGAAGGTCGAGACGTACACCCGAc > 2:773849/1‑86 (MQ=255)
aCGCACAAACGTCGTATCTCCGCACTCGGCCCAGGCGGTCTGACCCGTGAACGTGCAGGCTTCGAAGGTCGAGACGTACACCCGAc < 1:773849/86‑1 (MQ=255)
aCGCACAAACGTCGTATCTCCGCACTCGGCCCAGGCGGTCTGACCCGTGAACGTGCAGGCTTCGAAGGTCGAGACGTACACCCGACTCAc > 2:930453/1‑90 (MQ=255)
aCGCACAAACGTCGTATCTCCGCACTCGGCCCAGGCGGTCTGACCCGTGAACGTGCAGGCTTCGAAGGTCGAGACGTACACCCGACTCAc > 1:867599/1‑90 (MQ=255)
aCGCACAAACGTCGTATCTCCGCACTCGGCCCAGGCGGTCTGACCCGTGAACGTGCAGGCTTCGAAGGTCGAGACGTACACCCGACTCAc > 1:647949/1‑90 (MQ=255)
aCGCACAAACGTCGTATCTCCGCACTCGGCCCAGGCGGTCTGACCCGTGAACGTGCAGGCTTCGAAGGTCGAGACGTACACCCGACTCAc > 1:638835/1‑90 (MQ=255)
aCGCACAAACGTCGTATCTCCGCACTCGGCCCAGGCGGTCTGACCCGTGAACGTGCAGGCTTCGAAGGTCGAGACGTACACCCGACTCAc > 1:283170/1‑90 (MQ=255)
caAACGTCGTATCTCCGCACTCGGCCCAGGCGGTCTGACCCGTGAACGTGCAGGCTTCGAAGGTCGAGACGTACACCCGACTCACTACgg < 2:811362/90‑1 (MQ=255)
caAACGTCGTATCTCCGCACTCGGCCCAGGCGGTCTGACCCGTGAACGTGCAGGCTTCGAAGGTCGAGACGTACACCCGACTCACTACgg > 2:558580/1‑90 (MQ=255)
cgtATCTCCGCACTCGGCCCAGGCGGTCTGACCCGTGAACGTGCAGGCTTCGAAGGTCGAGACGTACACCCGACTCACTACGGTCGCGTa < 2:499295/90‑1 (MQ=255)
aTCTCCGCACTCGGCCCAGGCGGTCTGACCCGTGAACGTGCAGGCTTCGAAGGTCGAGACGTACACCCGACTCACTACGGTCGCGTATGt > 2:348002/1‑90 (MQ=255)
ctcCGCACTCGGCCCAGGCGCCCCGCCCCGTGAACGTGCAGGCTTCGAAGGTCGAGCCGTACCCCCGACTCCCTACGGTCGCGTATGTcc < 1:698179/90‑1 (MQ=255)
ccGCACTCGGCCCAGGCGGTCTGACCCGTGAACGTGCAGGCTTCGAAGGTCgaga > 1:171382/1‑55 (MQ=255)
ccGCACTCGGCCCAGGCGGTCTGACCCGTGAACGTGCAGGCTTCGAAGGTCgaga < 2:171382/55‑1 (MQ=255)
gCACTCGGCCCAGGCGGTCTGACCCGTGAACGTGCAGGCTTCGAAGGTCGAGACGTACACCCGACTCACTACGGTCGCGTATGTCCAATc > 1:792869/1‑90 (MQ=255)
gCACTCGGCCCAGGCGGTCTGACCCGTGAACGTGCAGGCTTCGAAGGTCGAGACGTACACCCGACTCACTACGGTCGCGTATGTCCAATc > 2:198169/1‑90 (MQ=255)
cTCGGCCCAGGCGGTCTGACCCGTGAACGTGCAGGCTTCGAAGGTCGAGACGTACACCCGACTCACTACGGTCGCGTATGTCCAATCGaa < 2:638835/90‑1 (MQ=255)
tCGGCCCAGGCGGTCTGACCCGTGAACGTGCAGGCTTCGAAGGTCGAGACGTACACCCGACTCACTACGGTCGCGTATGTCCAATCGaaa < 2:511170/90‑1 (MQ=255)
gCGGTCTGACCCGTGAACGTGCAGGCTTCGAAGGTCGAGACGTACACCCGACTCACTACGGTCGCGTATGTCCAATCGAAACCCCTGAAg < 1:29572/90‑1 (MQ=255)
ggTCTGACCCGTGAACGTGCAGGCTTCGAAGGTCGAGACGTACACCCGAc > 1:100261/1‑50 (MQ=255)
ggTCTGACCCGTGAACGTGCAGGCTTCGAAGGTCGAGACGTACACCCGAc < 2:100261/50‑1 (MQ=255)
ggTCTGACCCGTGAACGTGCAGGCTTCGAAGGTCGAGACGTACACCCGACTCACTACGGTCGCGTATGTCCAATCGAAACCCCTGAAGGt > 1:306723/1‑90 (MQ=255)
gTCTGACCCGTGAACGTGCAGGCTTCGAAGGTCGAGACGTACACCCGACTCACTACGGTCGCGTATGTCCAATCGAAACCCCTGAAGGTc < 1:122286/90‑1 (MQ=255)
tCTGACCCGTGAACGTGCAGGCTTCGAAGGTCGAGACGTACACCCGACTCACTACGGTCGCGTATGTCCAATCGAAACCCCTGAAGGTcc > 2:306842/1‑90 (MQ=255)
tCTGACCCGTGAACGTGCAGGCTTCGAAGGTCGAGACGTACACCCGACTCACTACGGTCGCGTATGTCCAATCGAAACCCCTGAAGGTcc > 2:478623/1‑90 (MQ=255)
tCTGACCCGTGAACGTGCAGGCTTCGAAGGTCGAGACGTACACCCGACTCACTACGGTCGCGTATGTCCAATCGAAACCCCTGAAGGTcc > 1:876723/1‑90 (MQ=255)
cTGACCCGTGAACGTGCAGGCTTCGAAGGTCGAGACGTACACCCGACTCACTACGGTCGCGTATGTCCAATCGAAACCCCTGAAGGTCCg < 2:560393/90‑1 (MQ=255)
gACCCGTGAACGTGCAGGCTTCGAAGGTCGAGACGTACACCCGACTCACTACGGTCGCGTATGTCCAATCGAAACCCCTGAAGGTCCGaa > 1:258175/1‑90 (MQ=255)
ccGTGAACGTGCAGGCTTCGAAGGTCGAGACGTACACCCGACTCACTACGGTCGCGTATGTCCAATCGAAACCCCTGAAGGTCCGAACAt < 1:198169/90‑1 (MQ=255)
gTGAACGTGCAGGCTTCGAAGGTCGAGACGTACACCCGACTCACTACGGTCGCGTATGTCCAATCGAAACCCCTGAAGGTCCGAACATCg > 2:759551/1‑90 (MQ=255)
aaCGTGCAGGCTTCGAAGTTCGAGACGTACACCCGACTCACTACGGTCGCGTATGTCCAATCGAAACCCCTGAAGGTCCGAACATCGGTc < 1:823949/90‑1 (MQ=255)
aaCGTGCAGGCTTCGAAGGTCGAGACGTACCCCCGACTCACTACGGTCGCGTATGTCCAATCGAAACCCCTGAAGGTCCGAACATCGGTc < 1:560821/90‑1 (MQ=255)
gCAGGCTTCGAAGGTCGAGACGTACACCCGACTCACTACGGTCGCGTATGTCCAATCGaa > 2:300241/1‑60 (MQ=255)
gCAGGCTTCGAAGGTCGAGACGTACACCCGACTCACTACGGTCGCGTATGTCCAATCGaa < 1:300241/60‑1 (MQ=255)
cAGGCTTCGAAGGTCGAGACGTACACCCGACTCACTACGGTCGCGTATGTCCAATCGAAACCCCTGAAGGTCCGAACATCGGTCTGATCa > 1:700496/1‑90 (MQ=255)
cAGGCTTCGAAGGTCGAGACGTACACCCGACTCACTACGGTCGCGTATGTCCAATCGAAACCCCTGAAGGTCCGAACATCGGTCTGATCa < 1:813923/90‑1 (MQ=255)
cAGGCTTCGAAGGTCGAGACGTACACCCGACTCACTACGGTCGCGTATGTCCAATCGAAACCCCTGAAGGTCCGAACATCGGTCTGATCa < 2:258175/90‑1 (MQ=255)
ggCTTCGAAGGTCGAGACGTACACCCGACTCACTACGGTCGCGTATGTCCAATCGAAACCCCTGAAGGTCCGAACATCGGTCTGATCAAc < 2:700496/90‑1 (MQ=255)
cTTCGAAGGTCGAGACGTACCCCCGACTCACTACGGTCGCGTATGTCCAATCGAAACCCCTGAAGGTCCGAACATCGGTCTGATCAActc < 2:541752/90‑1 (MQ=255)
cTTCGAAGGTCGAGACGTACCCCCGACTCACTACGGTCGCGTATGTCCAATCGAAACCCCTGAAGGTCCGAACATCGGTCTGATCAActc < 1:938126/90‑1 (MQ=255)
|
CAACCCGCTGTCTGAGATTACGCACAAACGTCGTATCTCCGCACTCGGCCCAGGCGGTCTGACCCGTGAACGTGCAGGCTTCGAAGTTCGAGACGTACACCCGACTCACTACGGTCGCGTATGTCCAATCGAAACCCCTGAAGGTCCGAACATCGGTCTGATCAACTC > NZ_CP009273/4172726‑4172893
|
| Alignment Legend |
|---|
Aligned base mismatch/match (shaded by quality score): ATCG/ATCG < 3 ≤ ATCG/ATCG < 17 ≤ ATCG/ATCG < 30 ≤ ATCG/ATCG < 35 ≤ ATCG/ATCG < 41 ≤ ATCG/ATCG |
Unaligned base: atcg Masked matching base: atcg Alignment gap: ‑ Deleted base: ‑ |
GATK/CNVnator alignment
BRESEQ :: bam2aln output
TTATGGACCAGAACAACCCGCTGTCTGAGATTACGCACAAACGTCGTATCTCCGCACTCGGCCCAGGCGGTCTGACCCGTGAACGTGCAGGCTTCGAAGTTCGAGACGTACACCCGACTCACTACGGTCGCGTATGTCCAATCGAAACCCCTGAAGGTCCGAACATCGGTCTGATCAACTCTCTGTCCGTGTACGCAC > NZ_CP009273/4172713‑4172910
|
TTATGGACCAGAACAACCCGCTGTCTGAGATTACGCACAAACGTCGTATCTCCGCACTCGGCCCAGGCGGTCTGACCCGTGAACGTGCAGGCTTCGAAGG > SRR3722023.508948/1‑100 (MQ=60)
GACCAGAACAACCCGCTGTCTGAGATTACGCACAAACGTCGTATCTCCGCACTCGGCCCAGGCGGTCTGACCCGTGAACGTGCAGGCTTCGAAGGTCGAG > SRR3722023.109890/1‑100 (MQ=60)
GAACAACCCGCTGTCTGAGATTACGCACAAACGTCGTATCTCCGCACTCGGCCCAGGCGGTCTGACCCGTGAACGTGCAGGCTTCGAAGGTCGAGACGTA > SRR3722023.852120/1‑100 (MQ=60)
GAACAACCCGCTGTCTGAGATTACGCACAAACGTCGTATCTCCGCACTCGGCCCAGGCGGTCTGACCCGTGAACGTGCAGGCTTCGAAGGTCGAGACGTA > SRR3722023.203297/1‑100 (MQ=60)
GAACAACCCGCTGTCTGAGATTACGCACAAACGTCGTATCTCCGCACTCGGCCCAGGCGGTCTGACCCGTGAACGTGCAGGCTTCGAAGGTCGAGACGTA > SRR3722023.351477/1‑100 (MQ=60)
CAACCCGCTGTCTGAGATTACGCACAAACGTCGTATCTCCGCACTCGGCCCAGGCGGTCTGACCCGTGAACGTGCAGGCTTCGAAGGTCGAGACGTACAC < SRR3722023.485919/100‑1 (MQ=60)
GTCTGAGATTACGCACAAACGTCGTATCTCCGCACTCGGCCCAGGCGGTCTGACCCGTGAACGTGCAGGCTTCGAAGGTCGAGACGTACACCCGACTCAC > SRR3722023.886192/1‑100 (MQ=60)
GTCTGAGATTACGCACAAACGTCGTATCTCCGCACTCGGCCCAGGCGGTCTGACCCGTGAACGTGCAGGCTTCGAAGGTCGAGACGTACACCCGACTCAC > SRR3722023.661411/1‑100 (MQ=60)
GTCTGAGATTACGCACAAACGTCGTATCTCCGCACTCGGCCCAGGCGGTCTGACCCGTGAACGTGCAGGCTTCGAAGGTCGAGACGTACACCCGACTCAC > SRR3722023.288402/1‑100 (MQ=60)
GTCTGAGATTACGCACAAACGTCGTATCTCCGCACTCGGCCCAGGCGGTCTGACCCGTGAACGTGCAGGCTTCGAAGGTCGAGACGTACACCCGACTCAC > SRR3722023.652072/1‑100 (MQ=60)
GATTACGCACAAACGTCGTATCTCCGCACTCGGCCCAGGCGGTCTGACCCGTGAACGTGCAGGCTTCGAAGGTCGAGACGTACACCCGACTCACTACGGT < SRR3722023.181511/100‑1 (MQ=60)
GATTACGCACAAACGTCGTATCTCCGCACTCGGCCCAGGCGGTCTGACCCGTGAACGTGCAGGCTTCGAAGGTCGAGACGTACACCCGACTCACTACGGT < SRR3722023.790340/100‑1 (MQ=60)
CGTCGTATCTCCGCACTCGGCCCAGGCGGTCTGACCCGTGAACGTGCAGGCTTCGAAGGTCGAGACGTACACCCGctgtctcttatacacatctgacgct > SRR3722023.174615/1‑75 (MQ=60)
TCGTATCTCCGCACTCGGCCCAGGCGGTCTGACCCGTGAACGTGCAGGCTTCGAAGGTCGAGACGTACACCCGACTCACTACGGTCGCGTATGTCCAATC > SRR3722023.809788/1‑100 (MQ=60)
CTCCGCACTCGGCCCAGGCGCCCCGCCCCGTGAACGTGCAGGCTTCGAAGGTCGAGCCGTACCCCCGACTCCCTACGGTCGCGTATGTCCAATCGAAACC < SRR3722023.712902/100‑1 (MQ=60)
cagatgtgtataagagacagCCGTGAACGTGCAGGCTTCGAAGGTCGAGACGTACACCCGACTCACTACGGTCGCGTATGTCCAATCGAAACCCCTGAAG < SRR3722023.305758/80‑1 (MQ=60)
CGGCCCAGGCGGTCTGACCCGTGAACGTGCAGGCTTCGAAGGTCGAGACGTACACCCGACTCACTACGGTCtgtctcttatacacatctgacgctgccga > SRR3722023.102062/1‑71 (MQ=60)
CGGCCCAGGCGGTCTGACCCGTGAACGTGCAGGCTTCGAAGGTCGAGACGTACACCCGACTCACTACGGTCGCGTATGTCCAATCGAAACCCCTGAAGGT > SRR3722023.312339/1‑100 (MQ=60)
GCCCAGGCGGTCTGACCCGTGAACGTGCAGGCTTCGAAGGTCGAGACGTACACCCGACTCACTACGGTCGCGTATGTCCAATCGAAACCCCTGAAGGTCC > SRR3722023.895500/1‑100 (MQ=60)
CAGGCGGTCTGACCCGTGAACGTGCAGGCTTCGAAGGTCGAGACGTACACCCGACTCACTACGGTCGCGTATGTCCAATCGAAACCCCTGAAGGTCCGAA > SRR3722023.262944/1‑100 (MQ=60)
GCGGTCTGACCCGTGAACGTGCAGGCTTCGAAGGTCGAGACGTACACCCGACTCACTACGGTCGCGTATGTCCAATCGAAACCCCTGAAGGTCCGAACAT < SRR3722023.30104/100‑1 (MQ=60)
GTCTGACCCGTGAACGTGCAGGCTTCGAAGGTCGAGACGTACACCCGACTCACTACGGTCGCGTATGTCCAATCGAAACCCCTGAAGGTCCGAACATCGG < SRR3722023.124533/100‑1 (MQ=60)
CCGTGAACGTGCAGGCTTCGAAGGTCGAGACGTACACCCGACTCACTACGGTCGCGTATGTCCAATCGAAACCCCTGAAGGTCCGAACATCGGTCTGATC < SRR3722023.201893/100‑1 (MQ=60)
CGTGAACGTGCAGGCTTCGAAGGTCGAGACGTACACCCGACTCACTACGGTCGCGTATGTCCAATCGAAACCCCTGAAGGTCCGAACATCGGTCTGATCA > SRR3722023.715268/1‑100 (MQ=60)
AACGTGCAGGCTTCGAAGTTCGAGACGTACACCCGACTCACTACGGTCGCGTATGTCCAATCGAAACCCCTGAAGGTCCGAACATCGGTCTGATCAACTC < SRR3722023.841589/100‑1 (MQ=60)
AACGTGCAGGCTTCGAAGGTCGAGACGTACCCCCGACTCACTACGGTCGCGTATGTCCAATCGAAACCCCTGAAGGTCCGAACATCGGTCTGATCAACTC < SRR3722023.571976/100‑1 (MQ=60)
CAGGCTTCGAAGGTCGAGACGTACACCCGACTCACTACGGTCGCGTATGTCCAATCGAAACCCCTGAAGGTCCGAACATCGGTCTGATCAACTCTCTGTC < SRR3722023.831346/100‑1 (MQ=60)
GGCTTCGAAGGTCGAGACGTACACCCGACTCACTACGGTCGCGTATGTCCAATCGAAACCCCTGAAGGTCCGAACATCGGTCTGATCAACTCTCTGTCCG > SRR3722023.826605/1‑100 (MQ=60)
CTTCGAAGGTCGAGACGTACCCCCGACTCACTACGGTCGCGTATGTCCAATCGAAACCCCTGAAGGTCCGAACATCGGTCTGATCAACTCTCTGTCCGTG < SRR3722023.958167/100‑1 (MQ=60)
GGTCGAGACGTACACCCGACTCACTACGGTCGCGTATGTCCAATCGAAACCCCTGAAGGTCCGAACATCGGTCTGATCAACTCTCTGTCCGTGTACGCAC < SRR3722023.519944/100‑1 (MQ=60)
GGTCGAGACGTACACCCGACTCACTACGGTCGCGTATGTCCAATCGAAACCCCTGAAGGTCCGAACATCGGTCTGATCAACTCTCTGTCCGTGTACGCAC < SRR3722023.28652/100‑1 (MQ=60)
|
TTATGGACCAGAACAACCCGCTGTCTGAGATTACGCACAAACGTCGTATCTCCGCACTCGGCCCAGGCGGTCTGACCCGTGAACGTGCAGGCTTCGAAGTTCGAGACGTACACCCGACTCACTACGGTCGCGTATGTCCAATCGAAACCCCTGAAGGTCCGAACATCGGTCTGATCAACTCTCTGTCCGTGTACGCAC > NZ_CP009273/4172713‑4172910
|
| Alignment Legend |
|---|
Aligned base mismatch/match (shaded by quality score): ATCG/ATCG < 0 ≤ ATCG/ATCG < 22 ≤ ATCG/ATCG < 31 ≤ ATCG/ATCG < 34 ≤ ATCG/ATCG < 41 ≤ ATCG/ATCG |
Unaligned base: atcg Masked matching base: atcg Alignment gap: ‑ Deleted base: ‑ |
