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 I0 R1
|
560 |
56.4 |
4650532 |
94.9% |
4413354 |
59.3 |
Breseq alignment
BRESEQ :: Evidence
|
| evidence |
seq id |
position |
mutation |
freq |
annotation |
gene |
description |
| RA |
W3110S.gb |
1,804,377 |
A→G |
22.4% |
intergenic (‑93/‑431) |
thrS ← / → arpB |
threonyl‑tRNA synthetase/ECK1718:JW5278:b1720; hypothetical protein, N‑ter fragment |
|
| |
seq id |
position |
ref |
new |
freq |
score (cons/poly) |
reads |
annotation |
genes |
product |
| * | W3110S.gb | 1,804,377 | 0 | A | G | 22.4%
| 126.9
/ 37.6
| 67 | intergenic (‑93/‑431) | thrS/arpB | threonyl‑tRNA synthetase/ECK1718:JW5278:b1720; hypothetical protein, N‑ter fragment |
| Reads supporting (aligned to +/- strand): ref base A (27/25); new base G (6/9); total (33/34) |
| Fisher's exact test for biased strand distribution p-value = 5.60e-01 |
| Kolmogorov-Smirnov test that lower quality scores support variant p-value = 9.25e-01 |
TGACCCACACGAAAGATCACATACAAAGAAAAATTTGTTTATTAACAGTTCATTGCGAAACCATCTAGCCAACAAATGCTAAATTGGTTCGCAATCAGGTACACAAATGAAAGACATTAACCTCTCACCTTCCACCC > W3110S.gb/1804307‑1804443
|
tgACCCACACGAAAGATCACATACAAAGAAAAATTTGTTTATTAACAGTTCATTGCGAAACCATCTAGCca < 1:4350206/71‑1 (MQ=255)
aCCCACACGAAAGATCACATACAAAGAAAAATTTGTTTATTAACAGTTCATTGCGAAACCATCTAGCcaa > 1:4183378/1‑70 (MQ=255)
cacaCGAAAGATCACATACAAAGAAAAATTTGTTTATTAACAGTTCATTGCGAAACCATCTAGCcgaca < 1:178241/69‑1 (MQ=255)
cacaCGAAAGATCACATACAAAGAAAAATTTGTTTATTAACAGTTCATTGCGAAACCATCTAGCCGACaaa < 1:4010534/71‑1 (MQ=255)
cacaCGAAAGATCACATACAAAGAAAAATTTGTTTATTAACAGTTCATTGCGAAACCATCTAGCCAACaaa < 1:2864778/71‑1 (MQ=255)
acGAAAGATCACATACAAAGAAAAATTTGTTTATTAACAGTTCATTGCGAAACCATCTAGCCAACaaa > 1:709804/1‑68 (MQ=255)
acGAAAGATCACATACAAAGAAAAATTTGTTTATTAACAGTTCATTGCGAAACCATCTAGCCAACAAATg > 1:2841197/1‑70 (MQ=255)
acGAAAGATCACATACAAAGAAAAATTTGTTTATTAACAGTTCATTGCGAAACCATCTAGCCAACAAATGc > 1:4607323/1‑71 (MQ=255)
cGAAAGATCACATACAAAGAAAAATTTGTTTATTAACAGTTCATTGCGAAACCATCTAGCCGACAAAt > 1:133062/1‑68 (MQ=255)
gAAAGATCACATACAAAGAAAAATTTGTTTATTAACAGTTCATTGCGAAACCATCTAGCCAACAAATGCTa < 1:4487511/71‑1 (MQ=255)
gAAAGATCACATACAAAGAAAAATTTGTTTATTAACAGTTCATTGCGAAACCATCTAGCCAACAAATGCTa < 1:4136417/71‑1 (MQ=255)
aTCACATACAAAGAAAAATTTGTTTATTAACAGTTCATTGCGAAACCATCTAGCCAACAAATGCTAAATTg < 1:2573190/71‑1 (MQ=255)
aTCACATACAAAGAAAAATTTGTTTATTAACAGTTCATTGCGAAACCATCTAGCCAACAAATGCTAAATTg > 1:2144990/1‑71 (MQ=255)
cacaTACAAAGAAAAATTTGTTTATTAACAGTTCATTGCGAAACCATCTAGCCAACAAATGCTa > 1:3389724/1‑64 (MQ=255)
acaTACAAAGAAAAATTTGTTTATTAACAGTTCATTGCGAAACCATCTAGCCAACAAATGCTAAATTGGtt > 1:4121265/1‑71 (MQ=255)
acaTACAAAGAAAAATTTGTTTATTAACAGTTCATTGCGAAACCATCTAGCCAACAAATGCTAAATTGGtt > 1:1949861/1‑71 (MQ=255)
caTACAAAGAAAAATTTGTTTATTAACAGTTCATTGCGAAACCATCTAGCCGACAAATGCTAAATTGGTTc > 1:3647894/1‑71 (MQ=255)
tACAAAGAAAAATTTGTTTATTAACAGTTCATTGCGAAACCATCTAGCCAACAAATGCTAAATTGGTTCGc < 1:1450429/71‑1 (MQ=255)
aCAAAGAAAAATTTGTTTATTAACAGTTCATTGCGAAACCATCTAGCCAACAAATGCTaaa > 1:3151914/1‑61 (MQ=255)
cAAAGAAAAATTTGTTTATTAACAGTTCATTGCGAAACCATCTAGCCGACAAATGCTAAATTGGTTCGCaa < 1:4186584/71‑1 (MQ=255)
cAAAGAAAAATTTGTTTATTAACAGTTCATTGCGAAACCATCTAGCCAACAAATGCTAAATTGGTTCGCaa > 1:54522/1‑71 (MQ=255)
cAAAGAAAAATTTGTTTATTAACAGTTCATTGCGAAACCATCTAGCCAACAAATGCTAAATTGGTTCGCaa > 1:1197501/1‑71 (MQ=255)
aaaGAAAAATTTGTTTATTAACAGTTCATTGCGAAACCATCTAGCCAACAAATGCTAAATTGGTTCGCaa < 1:1839112/70‑1 (MQ=255)
aaaaaTTTGTTTATTAACAGTTCATTGCGAAACCATCTAGCCAACAAATGCTAAATTGGTTCGCAATCAgg > 1:1976031/1‑71 (MQ=255)
aaaaaTTTGTTTATTAACAGTTCATTGCGAAACCATCTAGCCAACAAATGCTAAATTGGTTCGCAATCAgg < 1:3448375/71‑1 (MQ=255)
aaaaaTTTGTTTATTAACAGTTCATTGCGAAACCATCTAGCCAACAAATGCTAAATTGGTTCGCAATCAgg > 1:3371417/1‑71 (MQ=255)
aaaaTTTGTTTATTAACAGTTCATTGCGAAACCATCTAGCCGACAAATGCTAAATTgg > 1:2306738/1‑58 (MQ=255)
aaaTTTGTTTATTAACAGTTCATTGCGAAACCATCTAGCCAACAAATGCTAAATTg < 1:1912594/56‑1 (MQ=255)
aaaTTTGTTTATTAACAGTTCATTGCGAAACCATCTAGCCAACAAATGCTAAATTGGTTCGCAAt < 1:675321/65‑1 (MQ=255)
aTTTGTTTATTAACAGTTCATTGCGAAACCATCTAGCCGACAAATGCTAAATTGGt < 1:3667772/56‑1 (MQ=255)
aTTTGTTTATTAACAGTTCATTGCGAAACCATCTAGCCAACAAATGCTaa < 1:3763020/50‑1 (MQ=255)
aTTTGTTTATTAACAGTTCATTGCGAAACCATCTAGCCAACAAATGCTaa < 1:1054884/50‑1 (MQ=255)
aTTTGTTTATTAACAGTTCATTGCGAAACCATCTAGCCAACAAATGCTAAATTGGTTCGCAATCAGGTaca > 1:985514/1‑71 (MQ=255)
aTTTGTTTATTAACAGTTCATTGCGAAACCATCTAGCCAACAAATGCTAAATTGGTTCGCAATCAGGTaca > 1:2664812/1‑71 (MQ=255)
aTTTGTTTATTAACAGTTCATTGCGAAACCATCTAGCCAACAAATGCTAAATTGGTTCGCAATCAGGTac < 1:1795953/70‑1 (MQ=255)
tttGTTTATTAACAGTTCATTGCGAAACCATCTAGCCAACAAATGCTAAATTGGTTCGCAATCAGGTaca > 1:239588/1‑70 (MQ=255)
tttGTTTATTAACAGTTCATTGCGAAACCATCTAGCCAACAAATGCTAAATTGGTTCGCAATCAGGTaca > 1:522334/1‑70 (MQ=255)
tattatCAGTTCATTGCGAAACCATCTAGCCGACAAATGCTAAATTGGTTCGCAATCAGGTACACAAATg > 1:695871/1‑70 (MQ=255)
attaACAGTTCATTGCGAAACCATCTAGCCAACAAATGCTAAATTGGTTCGCAATCAGGTACACAAATGa > 1:4198848/1‑70 (MQ=255)
attaACAGTTCATTGCGAAACCATCTAGCCAACAAATGCTAAATTGGTTCGCAATCAGGTACACAAATGa < 1:1330168/70‑1 (MQ=255)
ttaACAGTTCATTGCGAAACCATCTAGCCAACAAATCCTAAATTGGTTCGCAATCAGGTACACAAATGaaa < 1:1201985/71‑1 (MQ=255)
taACAGTTCATTGCGAAACCATCTAGCCAACAAATGCTAAATTGGTTCGCAATCAGGTACACAAATGaaa < 1:2993258/70‑1 (MQ=255)
taACAGTTCATTGCGAAACCATCTAGCCAACAAATGCTAAATTGGTTCGCAATCAGGTACACAAATGa > 1:4476215/1‑68 (MQ=255)
aaCAGTTCATTGCGAAACCATCTAGCCAACAAATGCTAAATTGGTTCGCAATCAGGTACACAAATGAAAGa > 1:1822111/1‑71 (MQ=255)
aCAGTTCATTGCGAAACCATCTAGCCAACAAATGCTAAATTGGTTCGCAATCAGGTACACAAATGAAAg < 1:3877008/69‑1 (MQ=255)
gTTCATTGCGAAACCATCTAGCCGACAAATGCTAAATTGGTTCGCAATCAGGTACACAAATGAAAGACAtt < 1:2425666/71‑1 (MQ=255)
gTTCATTGCGAAACCATCTAGCCGACAAATGCTAAATTGGTTCGCAATCAGGTACACAAATGAAAGACAt < 1:856706/70‑1 (MQ=255)
gTTCATTGCGAAACCATCTAGCCAACAAATGCTAAATTGGTTCGCAATCAGGTACACAAATGAAAGACAtt < 1:3089765/71‑1 (MQ=255)
ttCATTGCGAAACCATCTAGCCAACAAATGCTAAATTGGt < 1:1784880/40‑1 (MQ=255)
ttCATTGCGAAACCATCTAGCCAACAAATGCTAAATTGGTTCGCAATCAGGTACACAAATGAAAGACAt < 1:4225844/69‑1 (MQ=255)
cATTGCGAAACCATCTAGCCAACAAATGCTAAATTGGTTCGCAATCAGGTACACAAATGAAAGACATTAAc > 1:645217/1‑71 (MQ=255)
aTTGCGAAACCATCTAGCCGACAAATGCTAAATTGGTTCGCAATCAGGTACACAAATGAAAGACATTa < 1:2324542/68‑1 (MQ=255)
aTTGCGAAACCATCTAGCCGACAAACGCTAAATTGGTTCGCAATCAGGTACACAAATGAAAGAc < 1:831364/64‑1 (MQ=255)
aTTGCGAAACCATCTAGCCAACAAATGCTAAATTGGTTCGCAATCAGGTACACAAATGAAAg < 1:3767517/62‑1 (MQ=255)
ttGCGAAACCATCTAGCCAACAAATGCTAAATTGGTTCGCAATCAGGTACACAAATGa < 1:105127/58‑1 (MQ=255)
tGCGAAACCATCTAGCCGACAAATGCTAAATTGGTTc > 1:3171323/1‑37 (MQ=255)
tGCGAAACCATCTAGCCGACAAATGCTAAATTGGTTCGCAATCAGGTACACAAATGAAAGACATTAACctc > 1:2639099/1‑71 (MQ=255)
cGAAACCATCTAGCCAACAAATGCTAAATTGGTTCGCAATCAGGTACACAAATGAAAGACATTAACCtctc < 1:984558/71‑1 (MQ=255)
gAAACCATCTAGCCGACAAATGCTAAATTGGTTCGCAATCAGGTATACAAATGAAAGACATTAACCTCTCa < 1:582516/71‑1 (MQ=255)
aaaCCATCTAGCCAACAAATGCTAAATTGGTTCGCAATCAGGTACACAAATGAAAGACATTAACCTCTCAc > 1:1252841/1‑71 (MQ=255)
cATCTAGCCGACAAATGCTAAATTGGTTCGCAATCAGGTACACAAATGAAAGACATTAACCTCTCACCTTc < 1:301331/71‑1 (MQ=255)
cATCTAGCCAACAAATGCTAAATTGGTTCGCAATCAGGTACACAAATGAAAGACATTAACCTCTCa < 1:3187328/66‑1 (MQ=255)
aTCTAGCCAACAAATGCTAAATTGGTTCGCAATCAGGTACACAAATGAAAGACATTaa > 1:367356/1‑58 (MQ=255)
tCTAGCCAACAAATGCTAAATTGGTTCGCAATCAGGTACACAAATGaaa < 1:45116/49‑1 (MQ=255)
tAGCCAACAAATGCTAAATTGGTTCGCAATCAGGTaca > 1:3514751/1‑38 (MQ=255)
tAGCCAACAAATGCTAAATTGGTTCGCAATCAGGTACACAAATGAAAGa > 1:1352253/1‑49 (MQ=255)
tAGCCAACAAATGCTAAATTGGTTCGCAATCAGGTACACAAATGAAAGa > 1:3617902/1‑49 (MQ=255)
tAGCCAACAAATGCTAAATTGGTTCGCAATCAGGTACACAAATGAAAGACa > 1:3847922/1‑51 (MQ=255)
aGCCAACAAATGCTAAATTGGTTCGCAATCAGGTACACAAATGAAAGACATTAACCTCTCACCTTcccccc > 1:1831721/1‑71 (MQ=255)
ccAACAAATGCTAAATTGGTTCGCAATCAGGTacac < 1:2714085/36‑1 (MQ=255)
caacaaATGCTAAATTGGTTCGCAATCAGGTAcaca < 1:2494431/36‑1 (MQ=255)
caacaaATGCTAAATTGGTTCGCAATCAGGTAcaca < 1:2950941/36‑1 (MQ=255)
aacaaATGCTAAATT‑GTTCGCAATCAGGTACACAAATGAAAGACATTa < 1:2268793/48‑1 (MQ=255)
|
TGACCCACACGAAAGATCACATACAAAGAAAAATTTGTTTATTAACAGTTCATTGCGAAACCATCTAGCCAACAAATGCTAAATTGGTTCGCAATCAGGTACACAAATGAAAGACATTAACCTCTCACCTTCCACCC > W3110S.gb/1804307‑1804443
|
| Alignment Legend |
|---|
Aligned base mismatch/match (shaded by quality score): ATCG/ATCG < 3 ≤ ATCG/ATCG < 21 ≤ ATCG/ATCG < 32 ≤ ATCG/ATCG < 36 ≤ ATCG/ATCG |
Unaligned base: atcg Masked matching base: atcg Alignment gap: ‑ Deleted base: ‑ |
GATK/CNVnator alignment
N/A
