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 I74 R1
|
158 |
13.7 |
815430 |
95.7% |
780366 |
86.0 |
Breseq alignment
BRESEQ :: Evidence
|
| evidence |
seq id |
position |
mutation |
annotation |
gene |
description |
| RA |
NZ_CP009273 |
4,525,805 |
A→G |
pseudogene (1198/1241 nt) |
yjhR → |
helicase YjhR |
|
| |
seq id |
position |
ref |
new |
freq |
score (cons/poly) |
reads |
annotation |
genes |
product |
| * | NZ_CP009273 | 4,525,805 | 0 | A | G | 100.0%
| 145.0
/ NA
| 42 | pseudogene (1198/1241 nt) | yjhR | helicase YjhR |
| Reads supporting (aligned to +/- strand): ref base A (0/0); new base G (17/25); total (17/25) |
CTGGTTCAGTGCTACACGGGAAGATAAGTATCAACGATACGATACGTCTTTGGTGTACCGTGGTGAAGGCGTAAAAAATGAAATAAAGGCAATATATGGTAGTCTGGATCAACGTCAGCTTTAAATGTGATGAGCCGTTCATGATACAGGAGTAGTAA > NZ_CP009273/4525725‑4525882
|
cTGGTTCAGTGCTACACGGGAAGATAAGTATCAACGATACGATACGTCTTTGGTGTACCGTGGTGAAGGCGTAAAAAATGGAATAAAGGc < 1:186738/90‑1 (MQ=255)
ggTTCAGTGCTACACGGGAAGATAAGTATCAACGATACGATACGTCTTTGGTGTACCGTGGTGAAGGCGTAAAAAATGGAATAAAGGCaa < 2:218918/90‑1 (MQ=255)
ggTTCAGTGCTACACGGGAAGATAAATATCAACGATACGATACGTCTTTGGTGTACCGTGGTGAAGGCGTAAAAAATGGAATAAAGGCaa < 1:207740/90‑1 (MQ=255)
gTTCAGTGCTACACGGGAAGATAAGTATCAACGATACGATACGTCTTTGGTGTACCGTGGTGAAGGCGTAAAAAATGGAATAAAGGCAat > 2:171041/1‑90 (MQ=255)
gTTCAGTGCTACACGGGAAGATAAGTATCAACGATACGATACGTCTTTGGTGTACCGTGGTGAAGGCGTAAAAAATGGAATAAAGGCAat > 1:121218/1‑90 (MQ=255)
gTTCAGTGCTACACGGGAAGATAAGTATCAACGATACGATACGTCTTTGGTGTACCGTGGTGAAGGCGTAAAAAATGGAATAAAGGCAat > 1:228031/1‑90 (MQ=255)
ttCAGCGCTACACGGGAAGATAAGTATCAACGATACGATACGTCTTTGGTGTACCGTGGTGAAGGCGTAAAAAATGGAATAAAGGCAata < 1:259543/90‑1 (MQ=255)
tGCTACACGGGAAGATAAGTATCAACGATACGATACGTCTTTGGTGTACCGTGGTGAAGGCGTAAAAAATGGAATAAAGGCAATATATgg < 2:355872/90‑1 (MQ=255)
tGCTACACGGGAAGATAAGTATCAACGATACGATACGTCTTTGGTGTACCGTGGTGAAGGCGTAAAAAATGGAATAAAGGCAATATATgg < 1:167829/90‑1 (MQ=255)
gCTACACGGGAAGATAAGTATCAACGATACGATACGTCTTTGGTGTACCGTGGTGAAGGCGTAAAAAATGGAATAAAGGCAATATATGGt < 2:20726/90‑1 (MQ=255)
acacGGGAAGATAAGTATCAACGATACGATACGTCTTTGGTGTACCGTGGTGAAGGCGTAAAAAATGGAATAAAGGCAATATATGGTAGt > 1:267461/1‑90 (MQ=255)
ggAAGATAAGTATCAACGATACGATACGTCTTTGGTGTACCGTGGTGAAGGCGTAAAAAATGGAATAAAGGc > 2:339097/1‑72 (MQ=255)
ggAAGATAAGTATCAACGATACGATACGTCTTTGGTGTACCGTGGTGAAGGCGTAAAAAATGGAATAAAGGc < 1:339097/72‑1 (MQ=255)
ggAAGATAAGTATCAACGATACGATACGTCTTTGGTGTACCGTGGTGAAGGCGTAAAAAATGGAATAAAGGCAATATATGGTAGTCTGGa > 2:349177/1‑90 (MQ=255)
ggAAGATAAGTATCAACGATACGATACGTCTTTGGTGTACCGTGGTGAAGGCGTAAAAAATGGAATAAAGGCAATATATGGTAGTCTGGa > 2:253531/1‑90 (MQ=255)
aGATAAGTATCAACGATACGATACGTCTTTGGTGTACCGTGGTGAAGGCGTAAAAAATGGAATAAAGGCAATATATGGTAGTCTGGATCa > 1:250264/1‑90 (MQ=255)
aaCGATACGATACGTCTTTGGTGTACCGTGGTGAAGGCGTAAAAAATGGAATAAAGGc > 1:236089/1‑58 (MQ=255)
aaCGATACGATACGTCTTTGGTGTACCGTGGTGAAGGCGTAAAAAATGGAATAAAGGc > 1:282016/1‑58 (MQ=255)
aaCGATACGATACGTCTTTGGTGTACCGTGGTGAAGGCGTAAAAAATGGAATAAAGGc < 2:282016/58‑1 (MQ=255)
aaCGATACGATACGTCTTTGGTGTACCGTGGTGAAGGCGTAAAAAATGGAATAAAGGc < 2:236089/58‑1 (MQ=255)
aaCGATACGATACGTCTTTGGTGTACCGTGGTGAAGGCGTAAAAAATGGAATAAAGGCAATATATGGTAGTCTGGATCAACGTCa > 1:373415/1‑85 (MQ=255)
aaCGATACGATACGTCTTTGGTGTACCGTGGTGAAGGCGTAAAAAATGGAATAAAGGCAATATATGGTAGTCTGGATCAACGTCa < 2:373415/85‑1 (MQ=255)
aaCGATACGATACGTCTTTGGTGTACCGTGGTGAAGGCGTAAAAAATGGAATAAAGGCAATATATGGTAGTCTGGATCAACGTCAGCttt > 2:97828/1‑90 (MQ=255)
gatacgatacGTCTTTGGTGTACCGTGGTGAAGGCGTAAAAAATGGAATAAAGGCAATATATGGTAGTCTGGATCAACGTCAGCTTTaaa < 2:183364/90‑1 (MQ=255)
gatacgatacGTCTTTGGTGTACCGTGGTGAAGGCGTAAAAAATGGAATAAAGGCAATATATGGTAGTCTGGATCAACGTCAGCTTTaaa < 1:271116/90‑1 (MQ=255)
cgTCTTTGGTGTACCGTGGTGAAGGCGTAAAAAATGGAATAAAGGCAata > 2:357919/1‑50 (MQ=255)
cgTCTTTGGTGTACCGTGGTGAAGGCGTAAAAAATGGAATAAAGGCAata < 1:357919/50‑1 (MQ=255)
gTCTTTGGTGTACCGTGGTGAAGGCGTAAAAAATGGAATAAAGGCAATATATGGTAGTCTGGATCAACGTCAGCTTTAAATGTGATGAGc < 1:256126/90‑1 (MQ=255)
tCTTTGGTGTACCGTGGTGAAGGCGTAAAAAATGGAATAAAGGCAATATATGGTAGTCTGGATCAACGTCAGCTTTAAATGTGATGAGcc > 2:392727/1‑90 (MQ=255)
tGGTGTACCGTGGTGAAGGCGTAAAAAATGGAATAAAGGCAATATATGGTAGTCTGGATCAACGTCAGCTTTAAATGTGATGAGCCGTTc < 2:250264/90‑1 (MQ=255)
tGGTGTACCGTGGTGAAGGCGTAAAAAATGGAATAAAGGCAATATATGGTAGTCTGGATCAACGTCAGCTTTAAATGTGATGAGCCGTTc < 1:226796/90‑1 (MQ=255)
gtgtACCGTGGTGAAGGCGTAAAAAATGGAATAAAGGCAATATATGGTAGTCTGGATCAACGTCAGCTTTAAATGTGATGAGCCGTTCAt < 1:349177/90‑1 (MQ=255)
ccGTGGTGAAGGCGTAAAAAATGGAATAAAGGCAATATATGGTAGTCTGGATCAACGTCAGCTTTAAATGTGATGAGCCGTTCATGATAc < 2:129667/90‑1 (MQ=255)
cGTGGTGAAGGCGTAAAAAATGGAATAAAGGCAATATATGGTAGTCTGGATCAACGTCAGCTTTAAATGTGATGAGCCGTTCATGATACa < 1:67859/90‑1 (MQ=255)
cGTGGTGAAGGCGTAAAAAATGGAATAAAGGCAATATATGGTAGTCTGGATCAACGTCAGCTTTAAATGTGATGAGCCGTTCATGATACa < 2:45409/90‑1 (MQ=255)
cGTGGTGAAGGCGTAAAAAATGGAATAAAGGCAATATATGGTAGTCTGGATCAACGTCAGCTTTAAATGTGATGAGCCGTTCATGATACa < 2:75803/90‑1 (MQ=255)
tggtgAAGGCGTAAAAAATGGAATAAAGGCAATATATGGTAGTCTGGATCAACGTCAGCTTTAAATGTGATGAGCCGTTCATGATACAgg < 1:227372/90‑1 (MQ=255)
tggtgAAGGCGTAAAAAATGGAATAAAGGCAATATATGGTAGTCTGGATCAACGTCAGCTTTAAATGTGATGAGCCGTTCATGATACAgg < 1:21695/90‑1 (MQ=255)
ggtgAAGGCGTAAAAAATGGAATAAAGGCAATATATGGTAGTCTGGATCAACGTCAGCTTTAAATGTGATGAGCCGTTCATGATACAGGa > 1:336793/1‑90 (MQ=255)
ggtgAAGGCGTAAAAAATGGAATAAAGGCAATATATGGTAGTCTGGATCAACGTCAGCTTTAAATGTGATGAGCCGTTCATGATACAGGa > 2:362700/1‑90 (MQ=255)
ggtgAAGGCGTAAAAAATGGAATAAAGGCAATATATGGTAGTCTGGATCAACGTCAGCTTTAAATGTGATGAGCCGTTCATGATACAGGa > 2:44290/1‑90 (MQ=255)
gCGTAAAAAATGGAATAAAGGCAATATATGGTAGTCTGGATCAACGTCAGCTTTAAATGTGATGAGCCGTTCATGATACAGGAGTAGTaa < 1:97828/90‑1 (MQ=255)
|
CTGGTTCAGTGCTACACGGGAAGATAAGTATCAACGATACGATACGTCTTTGGTGTACCGTGGTGAAGGCGTAAAAAATGAAATAAAGGCAATATATGGTAGTCTGGATCAACGTCAGCTTTAAATGTGATGAGCCGTTCATGATACAGGAGTAGTAA > NZ_CP009273/4525725‑4525882
|
| Alignment Legend |
|---|
Aligned base mismatch/match (shaded by quality score): ATCG/ATCG < 3 ≤ ATCG/ATCG < 31 ≤ ATCG/ATCG < 34 ≤ ATCG/ATCG < 36 ≤ ATCG/ATCG < 41 ≤ ATCG/ATCG |
Unaligned base: atcg Masked matching base: atcg Alignment gap: ‑ Deleted base: ‑ |
GATK/CNVnator alignment
BRESEQ :: bam2aln output
CTTTTAACTGGTTCAGTGCTACACGGGAAGATAAGTATCAACGATACGATACGTCTTTGGTGTACCGTGGTGAAGGCGTAAAAAATGAAATAAAGGCAATATATGGTAGTCTGGATCAACGTCAGCTTTAAATGTGATGAGCCGTTCATGATACAGGAGTAGTAAAGGGCATATT > NZ_CP009273/4525718‑4525892
|
CTTTTAACTGGTTCAGTGCTACACGGGAAGATAAGTATCAACGATACGATACGTCTTTGGTGTACCGTGGTGAAGGCGTAAAAAATGGAATAAAGGCAAT > SRR3722212.122620/1‑100 (MQ=60)
CTTTTAACTGGTTCAGTGCTACACGGGAAGATAAGTATCAACGATACGATACGTCTTTGGTGTACCGTGGTGAAGGCGTAAAAAATGGAATAAAGGCAAT > SRR3722212.230814/1‑100 (MQ=60)
agagacagGTGCTACACGGGAAGATAAGTATCAACGATACGATACGTCTTTGGTGTACCGTGGTGAAGGCGTAAAAAATGGAATAAAGGCAATATATGGT < SRR3722212.343802/92‑1 (MQ=60)
CTGGTTCAGTGCTACACGGGAAGATAAGTATCAACGATACGATACGTCTTTGGTGTACCGTGGTGAAGGCGTAAAAAATGGAATAAAGGCAATATATGGT < SRR3722212.188832/100‑1 (MQ=60)
GGTTCAGTGCTACACGGGAAGATAAATATCAACGATACGATACGTCTTTGGTGTACCGTGGTGAAGGCGTAAAAAATGGAATAAAGGCAATATATGGTAG < SRR3722212.210231/100‑1 (MQ=60)
GTTCAGTGCTACACGGGAAGATAAGTATCAACGATACGATACGTCTTTGGTGTACCGTGGTGAAGGCGTAAAAAATGGAATAAAGGCAATATATGGTAGT > SRR3722212.270903/1‑100 (MQ=60)
cgtgggctcggagatgtgtataagagacagCGATACGATACGTCTTTGGTGTACCGTGGTGAAGGCGTAAAAAATGGAATAAAGGCAATATATGGTAGTC < SRR3722212.362931/70‑1 (MQ=60)
TTCAGCGCTACACGGGAAGATAAGTATCAACGATACGATACGTCTTTGGTGTACCGTGGTGAAGGCGTAAAAAATGGAATAAAGGCAATATATGGTAGTC < SRR3722212.262853/100‑1 (MQ=60)
TGCTACACGGGAAGATAAGTATCAACGATACGATACGTCTTTGGTGTACCGTGGTGAAGGCGTAAAAAATGGAATAAAGGCAATATATGGTAGTCTGGAT < SRR3722212.169695/100‑1 (MQ=60)
CTACACGGGAAGATAAGTATCAACGATACGATACGTCTTTGGTGTACCGTGGTGAAGGCGTAAAAAATGGAATAAAGGCAATATATGGTAGTCTGGATCA > SRR3722212.253394/1‑100 (MQ=60)
GATAAGTATCAACGATACGATACGTCTTTGGTGTACCGTGGTGAAGGCGTAAAAAATGGAATAAAGGCAATATATGGTctgtctcttatacacatctccg > SRR3722212.238977/1‑78 (MQ=60)
GATAAGTATCAACGATACGATACGTCTTTGGTGTACCGTGGTGAAGGCGTAAAAAATGGAATAAAGGCAATATATGGTctgtctcttatacacatctccg > SRR3722212.285760/1‑78 (MQ=60)
GATAAGTATCAACGATACGATACGTCTTTGGTGTACCGTGGTGAAGGCGTAAAAAATGGAATAAAGGCAATATATGGTAGTCTGGATCAACGTCAGCTTT > SRR3722212.378657/1‑100 (MQ=60)
GATACGATACGTCTTTGGTGTACCGTGGTGAAGGCGTAAAAAATGGAATAAAGGCAATATATGGTAGTCTGGATCAACGTCAGCTTTAAATGTGATGAGC < SRR3722212.274633/100‑1 (MQ=60)
GTCTTTGGTGTACCGTGGTGAAGGCGTAAAAAATGGAATAAAGGCAATATATGGTAGTCTGGATCAACGTCAGCTTTAAATGTGATGAGCCGTTCATGAT < SRR3722212.259373/100‑1 (MQ=60)
TGGTGTACCGTGGTGAAGGCGTAAAAAATGGAATAAAGGCAATATATGGTAGTCTGGATCAACGTCAGCTTTAAATGTGATGAGCCGTTCATGATACAGG < SRR3722212.229561/100‑1 (MQ=60)
GGTGTACCGTGGTGAAGGCGTAAAAAATGGAATAAAGGCAATATATGGTAGTCTGGATCAACGTCAGCTTTAAATGTGATGAGCCGTTCATGATACAGGA > SRR3722212.341467/1‑100 (MQ=60)
GTGTACCGTGGTGAAGGCGTAAAAAATGGAATAAAGGCAATATATGGTAGTCTGGATCAACGTCAGCTTTAAATGTGATGAGCCGTTCATGATACAGGAG < SRR3722212.354060/100‑1 (MQ=60)
CGTGGTGAAGGCGTAAAAAATGGAATAAAGGCAATATATGGTAGTCTGGATCAACGTCAGCTTTAAATGTGATGAGCCGTTCATGATACAGGAGTAGTAA < SRR3722212.68685/100‑1 (MQ=60)
TGGTGAAGGCGTAAAAAATGGAATAAAGGCAATATATGGTAGTCTGGATCAACGTCAGCTTTAAATGTGATGAGCCGTTCATGATACAGGAGTAGTAAAG < SRR3722212.230146/100‑1 (MQ=60)
TGGTGAAGGCGTAAAAAATGGAATAAAGGCAATATATGGTAGTCTGGATCAACGTCAGCTTTAAATGTGATGAGCCGTTCATGATACAGGAGTAGTAAAG < SRR3722212.21960/100‑1 (MQ=60)
GCGTAAAAAATGGAATAAAGGCAATATATGGTAGTCTGGATCAACGTCAGCTTTAAATGTGATGAGCCGTTCATGATACAGGAGTAGTAAAGGGCATATT < SRR3722212.98987/100‑1 (MQ=60)
|
CTTTTAACTGGTTCAGTGCTACACGGGAAGATAAGTATCAACGATACGATACGTCTTTGGTGTACCGTGGTGAAGGCGTAAAAAATGAAATAAAGGCAATATATGGTAGTCTGGATCAACGTCAGCTTTAAATGTGATGAGCCGTTCATGATACAGGAGTAGTAAAGGGCATATT > NZ_CP009273/4525718‑4525892
|
| Alignment Legend |
|---|
Aligned base mismatch/match (shaded by quality score): ATCG/ATCG < 0 ≤ ATCG/ATCG < 31 ≤ ATCG/ATCG < 34 ≤ ATCG/ATCG < 35 ≤ ATCG/ATCG < 41 ≤ ATCG/ATCG |
Unaligned base: atcg Masked matching base: atcg Alignment gap: ‑ Deleted base: ‑ |
