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 F2 I194 R1
|
197 |
32.2 |
1845014 |
95.2% |
1756453 |
85.4 |
Breseq alignment
BRESEQ :: Evidence
|
| evidence |
seq id |
position |
mutation |
annotation |
gene |
description |
| RA |
NZ_CP009273 |
2,623,127 |
(T)5→4 |
intergenic (+287/‑24) |
yfgG → / → yfgH |
YfgG family protein/glycine zipper 2TM domain‑containing protein |
|
| |
seq id |
position |
ref |
new |
freq |
score (cons/poly) |
reads |
annotation |
genes |
product |
| * | NZ_CP009273 | 2,623,123 | 0 | T | . | 92.3%
| 84.7
/ 3.0
| 26 | intergenic (+283/‑28) | yfgG/yfgH | YfgG family protein/glycine zipper 2TM domain‑containing protein |
| Reads supporting (aligned to +/- strand): ref base T (1/1); new base . (13/11); total (14/12) |
| Fisher's exact test for biased strand distribution p-value = 1.00e+00 |
| Kolmogorov-Smirnov test that lower quality scores support variant p-value = 7.30e-01 |
TGCGTGAATTTTAATAAATTTAATCTATCCCTTTATACGCAATACATTTACTTTCCTCTTTTGATGATCTTAAATGTCTTATTTTTCGTAATGTGTATAACAAGGAATAGTGATGAAATTTAAAAAATGTCTTCTGCCTGTGGCAATGTTAGCGTCATTCACTC > NZ_CP009273/2623042‑2623205
|
tGCGTGAATTTTAATAAATTTAATCTATCCCTTTATACGCAATACATTTACTTTCCTCTTTTGATGATCTTAAATGTCTTA‑TTTTCGTaa < 1:142411/90‑1 (MQ=255)
aTCCCTTTATACGCAATACATTTACTTTCCTCTTTTGATGATCTTAAATGTCTTA‑TTTTCGTAATGTGTATAACAAGGAATAGTGATGaa > 1:294495/1‑90 (MQ=255)
tttATACGCAATACATTTACTTTCCTCTTTTGATGATCTTAAATGTCTTA‑TTTTCGTaa > 1:622800/1‑59 (MQ=255)
tttATACGCAATACATTTACTTTCCTCTTTTGATGATCTTAAATGTCTTA‑TTTTCGTaa < 2:622800/59‑1 (MQ=255)
tataCGCAATACATTTACTTTCCTCTTTTGATGATCTTAAATGTCTTA‑TTTTCGTAATGTGTATAACAAGGAATAGTGATGAAATTTaaa < 1:167386/90‑1 (MQ=255)
ataCGCAATACATTTACTTTCCTCTTTTGATGATCTTAAATGTCTTA‑TTTTCGTAATGTGTATAACAAGGAATAGTGATGAAATTTaaaa > 2:883975/1‑90 (MQ=255)
cAATACATTTACTTTCCTCTTTTGATGATCTTAAATGTCTTATTTTTCGTAATGTGTATAACAAGGAATAGTGATGAAATTTAAAAAATg > 2:615270/1‑90 (MQ=255)
cAATACATTTACTTTCCTCTTTTGATGATCTTAAATGTCTTA‑TTTTCGTAATGTGTATAACAAGGAATAGTGATGAAATTTAAAAAATGt > 1:396746/1‑90 (MQ=255)
gaTACATTTAGTGTCCTCTTTTGGTGATGTTAAATGTCTTA‑TTTTCGTAATGGGTATAACAAGGAATATGGAGAAAATTTAAAAAGTGtc > 1:733103/2‑90 (MQ=255)
aTACATTTACTTTCCTCTTTTGATGATCTTAAATGTCTTA‑TTTTCGTAATGTGTATAACAAGGAATAGTGATGAAATTTAAAAAATGtct > 1:415470/1‑90 (MQ=255)
aCATTTACTTTCCTCTTTTGATGATCTTAAATGTCTTA‑TTTTCGTAATGTGTATAACAAGGAATAGTGATGAAATTTAAAAAATGtcttc < 1:130747/90‑1 (MQ=255)
cATTTACTTTCCTCTTTTGATGATCTTAAATGTCTTATTTTTCGTAATGTGTATAACAAGGAATAGTGATGAAATTTAAAAAATGtcttc < 1:615270/90‑1 (MQ=255)
aCTTTCCTCTTTTGATGATCTTAAATGTCTTA‑TTTTCGTAATGTGTATaa > 1:759454/1‑50 (MQ=255)
aCTTTCCTCTTTTGATGATCTTAAATGTCTTA‑TTTTCGTAATGTGTATaa < 2:759454/50‑1 (MQ=255)
aCTTTCCTCTTTTGATGATCTTAAATGTCTTA‑TTTTCGTAATGTGTATAACAAGGAATAGTGATGAAATTTAAAAAATGTCTTCTGCCtg > 1:670708/1‑90 (MQ=255)
tttCCTCTTTTGATGATCTTAAATGTCTTA‑TTTTCGTAATGTGTATAACAAGGAATAGTGATGAAATTTAAAAAATGTCTTCTGCCtgtg > 2:229897/1‑90 (MQ=255)
ttCCTCTTTTGATGATCTTAAATGTCTTA‑TTTTCGTaa > 1:915653/1‑38 (MQ=38)
ttCCTCTTTTGATGATCTTAAATGTCTTA‑TTTTCGTaa < 2:915653/38‑1 (MQ=38)
tCCTCTTTTGATGATCTTAAATGTCTTA‑TTTTCGTAAt > 1:696878/1‑38 (MQ=38)
tCCTCTTTTGATGATCTTAAATGTCTTA‑TTTTCGTAAt < 2:696878/38‑1 (MQ=38)
ccTCTTTTGATGATCTTAAATGTCTTA‑TTTTCGTAAtg > 2:380195/1‑38 (MQ=38)
ccTCTTTTGATGATCTTAAATGTCTTA‑TTTTCGTAAtg < 1:380195/38‑1 (MQ=38)
tCTTAAATGTCTTA‑TTTTCGTAATGTGTATAACaa > 2:43134/1‑35 (MQ=255)
tCTTAAATGTCTTA‑TTTTCGTAATGTGTATAACaa < 1:43134/35‑1 (MQ=255)
ttAAATGTCTTA‑TTTTCGTAATGTGTATAACAAGGAATAGTGATGAAATTTAAAAAATGTCTTCTGCCTGTGGCAATGTTAGCGTCATTc < 1:883975/90‑1 (MQ=255)
aTGTCTTA‑TTTTCGTAATGTGTATAACAAGGAATAGTGATGAAATTTAAAAAATGTCTTCTGCCTGTGGCAATGTTAGCGTCATTCActc < 2:586528/90‑1 (MQ=255)
|
TGCGTGAATTTTAATAAATTTAATCTATCCCTTTATACGCAATACATTTACTTTCCTCTTTTGATGATCTTAAATGTCTTATTTTTCGTAATGTGTATAACAAGGAATAGTGATGAAATTTAAAAAATGTCTTCTGCCTGTGGCAATGTTAGCGTCATTCACTC > NZ_CP009273/2623042‑2623205
|
| Alignment Legend |
|---|
Aligned base mismatch/match (shaded by quality score): ATCG/ATCG < 3 ≤ ATCG/ATCG < 24 ≤ ATCG/ATCG < 31 ≤ ATCG/ATCG < 37 ≤ ATCG/ATCG < 41 ≤ ATCG/ATCG |
Unaligned base: atcg Masked matching base: atcg Alignment gap: ‑ Deleted base: ‑ |
GATK/CNVnator alignment
BRESEQ :: bam2aln output
TGCGTGAATTTTAATAAATTTAATCTATCCCTTTATACGCAATACATTTACTTTCCTCTTTTGATGATCTTAAATGTCTTATTTTTCGTAATGTGTATAACAAGGAATAGTGATGAAATTTAAAAAATGTCTTCTGCCTGTGGCAATGTTAGCGTCATTCACTCTGGCAGGATGCCAGTCAAAT > NZ_CP009273/2623042‑2623225
|
TGCGTGAATTTTAATAAATTTAATCTATCCCTTTATACGCAATACATTTACTTTCCTCTTTTGATGATCTTAAATGTCTTA‑TTTTCGTAATGTGTATAAC < SRR3722072.144958/100‑1 (MQ=60)
aatcggacgtctcgtgggctcggagatgtgtataagagacagCATTTACTTTCCTCTTTTGATGATCTTAAATGTCTTA‑TTTTCGTAATGTGTATAACAA < SRR3722072.386988/58‑1 (MQ=60)
gataatcggacgtctcgtgggctcggagatgtgtataagagacagCTTTTGATGATCTTAAATGTCTTA‑TTTTCGTAATGTGTATAACAAGGAATAGTGA < SRR3722072.43925/55‑1 (MQ=60)
AATTTAATCTATCCCTTTATACGCAATACATTTACTTTCCTCTTTTGATGATCTTAAATGTCTTA‑TTTTCGTAATGTGTATAACAAGGAATAGTGATGAA > SRR3722072.299589/1‑100 (MQ=60)
AATCTATCCCTTTATACGCAATACATTTACTTTCCTCTTTTGATGATCTTAAATGTCTTA‑TTTTCGTAATGTGTATAACctgtctcttatacacatctcc > SRR3722072.633914/1‑79 (MQ=60)
CCTTTATACGCAATACATTTACTTTCCTCTTTTGATGATCTTAAATGTCTTA‑TTTTCGTAATGTGTATAACAAGGAATAGTGATGAAATTTAAAAAATGT > SRR3722072.403905/1‑100 (MQ=60)
TTTATACGCAATACATTTACTTTCCTCTTTTGATGATCTTAAATGTCTTA‑TTTTCGTAATGTGTATAACAAGGAATAGTGATGAAATTTAAAAAATGTCT > SRR3722072.422991/1‑100 (MQ=60)
TATACGCAATACATTTACTTTCCTCTTTTGATGATCTTAAATGTCTTA‑TTTTCGTAATGTGTATAACAAGGAATAGTGATGAAATTTAAAAAATGTCTTC < SRR3722072.170280/100‑1 (MQ=60)
CAATACATTTACTTTCCTCTTTTGATGATCTTAAATGTCTTA‑TTTTCGTAATGTGTATAACAAGGAATAGctgtctcttatacacatctccgagcccacg > SRR3722072.772843/1‑70 (MQ=60)
CAATACATTTACTTTCCTCTTTTGATGATCTTAAATGTCTTA‑TTTTCGTAATGTGTATAACAAGGAATAGTGATGAAATTTAAAAAATGTCTTCTGCCTG > SRR3722072.682715/1‑100 (MQ=60)
TACATTTACTTTCCTCTTTTGATGATCTTAAATGTCTTA‑TTTTCGTAATGTGTATAACctgcctcttatacacatctccgagcccacgagacgtccgatt > SRR3722072.931391/1‑58 (MQ=60)
ACATTTACTTTCCTCTTTTGATGATCTTAAATGTCTTA‑TTTTCGTAATGTGTATAACActgtctcttatacacatctccgagcccacgagacgtccgatt > SRR3722072.709346/1‑58 (MQ=60)
ACATTTACTTTCCTCTTTTGATGATCTTAAATGTCTTA‑TTTTCGTAATGTGTATAACAAGGAATAGTGATGAAATTTAAAAAATGTCTTCTGCCTGTGGC < SRR3722072.133097/100‑1 (MQ=60)
CATTTACTTTCCTCTTTTGATGATCTTAAATGTCTTATTTTTCGTAATGTGTATAACAAGGAATAGTGATGAAATTTAAAAAATGTCTTCTGCCTGTGGC < SRR3722072.626237/100‑1 (MQ=60)
TCTTAAATGTCTTA‑TTTTCGTAATGTGTATAACAAGGAATAGTGATGAAATTTAAAAAATGTCTTCTGCCTGTGGCAATGTTAGCGTCATTCACTCTGGC > SRR3722072.155112/1‑100 (MQ=60)
TCTTAAATGTCTTA‑TTTTCGTAATGTGTATAACAAGGAATAGTGATGAAATTTAAAAAATGTCTTCTGCCTGTGGCAATGTTAGCGTCATTCACTCTGGC > SRR3722072.903693/1‑100 (MQ=60)
CTTAAATGTCTTA‑TTTTCGTAATGTGTATAACAAGGAATAGTGATGAAATTTAAAAAATGTCTTCTGCCTGTGGCAATGTTAGCGTCATTCACTCTGGCA > SRR3722072.2599/1‑100 (MQ=60)
TTAAATGTCTTA‑TTTTCGTAATGTGTATAACAAGGAATAGTGATGAAATTTAAAAAATGTCTTCTGCCTGTGGCAATGTTAGCGTCATTCACTCTGGCAG < SRR3722072.899192/100‑1 (MQ=60)
GTCTTA‑TTTTCGTAATGTGTATAACAAGGAATAGTGActgtctcttatacacatctccgagcccacgagacgtccgattatctcgtatgccgtcttctgc > SRR3722072.561160/1‑37 (MQ=60)
TTCGTAATGTGTATAACAAGGAATAGTGATGAAATTTAAAAAATGTCTTCTGCCTGTGGCAATGTTAGCGTCATTCACTCTGGCAGGATGCCAGTCAAAT > SRR3722072.386542/1‑100 (MQ=60)
|
TGCGTGAATTTTAATAAATTTAATCTATCCCTTTATACGCAATACATTTACTTTCCTCTTTTGATGATCTTAAATGTCTTATTTTTCGTAATGTGTATAACAAGGAATAGTGATGAAATTTAAAAAATGTCTTCTGCCTGTGGCAATGTTAGCGTCATTCACTCTGGCAGGATGCCAGTCAAAT > NZ_CP009273/2623042‑2623225
|
| Alignment Legend |
|---|
Aligned base mismatch/match (shaded by quality score): ATCG/ATCG < 0 ≤ ATCG/ATCG < 30 ≤ ATCG/ATCG < 34 ≤ ATCG/ATCG < 37 ≤ ATCG/ATCG < 41 ≤ ATCG/ATCG |
Unaligned base: atcg Masked matching base: atcg Alignment gap: ‑ Deleted base: ‑ |
