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 I195 R1
|
222 |
27.1 |
1551108 |
96.0% |
1489063 |
86.0 |
Breseq alignment
BRESEQ :: Evidence
|
| evidence |
seq id |
position |
mutation |
annotation |
gene |
description |
| RA |
NZ_CP009273 |
2,029,236 |
T→C |
intergenic (+512/‑80) |
ompC → / → hchA |
porin OmpC/protein deglycase HchA |
|
| |
seq id |
position |
ref |
new |
freq |
score (cons/poly) |
reads |
annotation |
genes |
product |
| * | NZ_CP009273 | 2,029,236 | 0 | T | C | 95.7%
| 144.7
/ ‑2.2
| 46 | intergenic (+512/‑80) | ompC/hchA | porin OmpC/protein deglycase HchA |
| Reads supporting (aligned to +/- strand): ref base T (0/2); new base C (21/23); total (21/25) |
| Fisher's exact test for biased strand distribution p-value = 4.93e-01 |
| Kolmogorov-Smirnov test that lower quality scores support variant p-value = 9.98e-01 |
GCGTGAATAATATTCAACACCAGTGCAGCATCATCATTACATACTTACAGCCGCCGACTACCGCTTTCGATATATTGACTCAATTTTCCAGCCTGGTTAAAAATAGCGACCAGCTCAGTCGCAAATATAGTGACTACCCTAACTAAGCAACAATAAGGAATACACT > NZ_CP009273/2029150‑2029315
|
gCGTGAATAATATTCAACACCAGTGCAGCATCATCATTACATACTTACAGCCGCCGACTACCGCTTTCGATATATTGACTCAATTTCCCa > 2:141293/1‑90 (MQ=255)
gCGTGAATAATATTCAACACCAGTGCAGCATCATCATTACATACTTACAGCCGCCGACTACCGCTTTCGATATATTGACTCAATTTCCCa > 1:185530/1‑90 (MQ=255)
gAATAATATTCAACACCAGTGCAGCATCATCATTACATACTTACAGCCGCCGACTACCGCTTTCGATATATTGACTCAATTTCCCAGCCt < 2:621626/90‑1 (MQ=255)
cAACACCAGTGCAGCATCATCATTACATACTTACAGCCGCCGACTACCGCTTTCGATATATTGACTCAATTTCCCAGCCTGGTTAAAAAt > 2:753851/1‑90 (MQ=255)
cAACACCAGTGCAGCATCATCATTACATACTTACAGCCGCCGACTACCGCTTTCGATATATTGACTCAATTTCCCAGCCTGGTTAAAAAt > 2:204092/1‑90 (MQ=255)
cAACACCAGTGCAGCATCATCATTACATACTTACAGCCGCCGACTACCGCTTTCGATATATTGACTCAATTTCCCAGCCTGGTTAAAAAt > 1:27836/1‑90 (MQ=255)
cAACACCAGTGCAGCATCATCATTACATACTTACAGCCGCCGACTACCGCTTTCGATATATTGACTCAATTTCCCAGCCTGGTTAAAAAt > 2:611552/1‑90 (MQ=255)
aGTGCAGCATCATCATTACATACTTACAGCCGCCGACTACCGCTTTCGATATATTGACTCAATTTCCCAGCCTGGTTAAAAATAGCGAcc > 2:627226/1‑90 (MQ=255)
aGTGCAGCATCATCATTACATACTTACAGCCGCCGACTACCGCTTTCGATATATTGACTCAATTTCCCAGCCTGGTTAAAAATAGCGAcc < 2:195629/90‑1 (MQ=255)
aGTGCAGCATCATCATTACATACTTACAGCCGCCGACTACCGCTTTCGATATATTGACTCAATTTCCCAGCCGGGTTAAAAATAGCGAcc > 2:110086/1‑90 (MQ=255)
gTGCAGCATCATCATTACATACTTACAGCCGCCGACTACCGCTTTCGATATATTGACTCAATTTCCCAGCCTGGTTAAAAATAGCGACCa > 1:167037/1‑90 (MQ=255)
tcatcatTACATACTTACAGCCGCCGACTACCGCTTTCGATATATTGACTCAATTTCCCAGCCTGGTTAAAAATAGCGACCAGCTCAGTc < 2:149907/90‑1 (MQ=255)
atcatTACATACTTACAGCCGCCGACTACCGCTTTCGATATATTGACTCAATTTCCCAGCCTGGTTAAAAATAGCGACCAGCTCAGTCGc > 2:580969/1‑90 (MQ=255)
atcatTACATACTTACAGCCGCCGACTACCGCTTTCGATATATTGACTCAATTTCCCAGCCTGGTTAAAAATAGCGACCAGCTCAGTCGc > 1:383973/1‑90 (MQ=255)
atcatTACATACTTACAGCCGCCGACTACCGCTTTCGATATATTGACTCAATTTCCCAGCCTGGTTAAAAATAGCGACCAGCTCAGTCGc < 1:627226/90‑1 (MQ=255)
catTACATACTTACAGCCGCCGACTACCGCTTTCGATATATTGACTCAATTTCCCAGCCTGGTTAAAAATAGCGACCAGCTCAGTCGCaa < 1:634848/90‑1 (MQ=255)
tACATACTTACAGCCGCCGACTACCGCTTTCGATATATTGACTCAATTTCCCAGCCTGGTTAAAAATAGCGACCAGCTCAGTCGCAAata > 2:105122/1‑90 (MQ=255)
cATACTTACAGCCGCCGACTACCGCTTTCGATATATTGACTCAATTTCCCAGCCTGGTTAAAAATAGCGACCAGCTCAGTCGCAAAtata < 1:510554/90‑1 (MQ=255)
cATACTTACAACCGCCGACTACCGCTTTCGATATATTGACTCAATTTCCCAGCCTGGTTAAAAATAGCGACCAGCTCAGTCGCAAAtata < 1:505112/90‑1 (MQ=255)
aTACTTACAGCCGCCGACTACCGCTTTCGATATATTGACTCAATTTCCCAGCCTGGTTAAAAATAGCGACCAGCTCAGTCGCAAATATAg > 1:300905/1‑90 (MQ=255)
cTTACAGCCGCCGACTACCGCTTTCGATATATTGACTCAATTTCCCAGCCTGGTTAAAAATAGCGACCAGCTCAGTCGCAAATATAGTGa < 2:300905/90‑1 (MQ=255)
cTTACAGCCGCCGACTACCGCTTTCGATATATTGACTCAATTTCCCAGCCTGGTTAAAAATAGCGACCAGCTCAGTCGCAAATATAGTGa < 1:539473/90‑1 (MQ=255)
cTTACAGCCGCCGACTACCGCTTTCGATATATTGACTCAATTTCCCAGCCTGGTTAAAAATAGCGACCAGCTCAGTCGCAAATATAGTGa < 1:355032/90‑1 (MQ=255)
cTTACAGCCGCCGACTACCGCTTTCGATATATTGACTCAATTTCCCAGCCTGGTTAAAAATAGCGACCAGCTCAGTCGCAAATATAGTGa > 2:157668/1‑90 (MQ=255)
ttACAGCCGCCGACTACCGCTTTCGATATATTGACTCAATTTCCCAGCCTGGTTAAAAATAGCGACCAGCTCAGTCGCAAATATAGTGAc < 2:257558/90‑1 (MQ=255)
ttACAGCCGCCGACTACCGCTTTCGATATATTGACTCAATTTCCCAGCCTGGTTAAAAATAGCGACCAGCTCAGTCGCAAATATAGTGAc > 2:166615/1‑90 (MQ=255)
aGCCGCCGACTACCGCTTTCGATATATTGACTCAATTTCCCAGCCTGGTTAAAAATAGCGACCAGCTCAGTCGCAAATATAGTGACTAcc > 1:622622/1‑90 (MQ=255)
cgccgACTACCGCTTTCGATATATTGACTCAATTTCCCAGCCTGGTTAAAAATAGCGACCAGCTCAGTCGCAAATATAGTGACTACCcta > 1:765481/1‑90 (MQ=255)
cgccgACTACCGCTTTCGATATATTGACTCAATTTCCCAGCCTGGTTAAAAATAGCGACCAGCTCAGTCGCAAATATAGTGACTACCcta > 1:131520/1‑90 (MQ=255)
gccgACTACCGCTTTCGATATATTGACTCAATTTCCCAGCCTGGTTAAAAATAGCGACCAGCTCAGTCGCAAATATAGTGACTACCctaa > 2:528788/1‑90 (MQ=255)
ccgACTACCGCTTTCGATATATTGACTCAATTTCCCAGCCTGGTTAAAAATAGCGACCAGCTCAGTCGCAAATATAGTGACTACCctaac < 1:675507/90‑1 (MQ=255)
tACCGCTTTCGATATATTGACTCAATTTTCCAGCCTGGTTAAAAATAGCGACCAGCTCAGTCGCAAATATAGTGACTACCCTAACTAAGc < 1:379676/90‑1 (MQ=255)
tACCGCTTTCGATATATTGACTCAATTTCCCAGCCTGGTTAAAAATAGCGACCAGCTCAGTCGCAAATATAGTGACTACCCTAACTAAGc < 2:44790/90‑1 (MQ=255)
tACCGCTTTCGATATATTGACTCAATTTCCCAGCCTGGTTAAAAATAGCGACCAGCTCAGTCGCAAATATAGTGACTACCCTAACTAAGc < 1:250453/90‑1 (MQ=255)
tACCGCTTTCGATATATTGACTCAATTTCCCAGCCTGGTTAAAAATAGCGACCAGCTCAGTCGCAAATATAGTGACTACCCTAACTAAGc < 1:611552/90‑1 (MQ=255)
cGCTTTCGATATATTGACTCAATTTCCCAGCCTGGTTAAAAATAGCGACCAGCTCAGTCGCAAATATAGTGACTACCCTAACTAAGcaac < 2:27836/90‑1 (MQ=255)
ttCGATATATTGACTCAATTTCCCAGCCTGGTTAAAAATAGCGACCAGCTCAGTCGCAAATATAGTGACTACCCTAACTAAGCAACAATa < 2:383973/90‑1 (MQ=255)
ttCGATATATTGACTCAATTTCCCAGCCTGGTTAAAAATAGCGACCAGCTCAGTCGCAAATATAGTGACTACCCTAACTAAGCAACAATa < 1:186651/90‑1 (MQ=255)
ttCGATATATTGACTCAATTTCCCAGCCTGGTTAAAAATAGCGACCAGCTCAGTCGCAAATATAGTGACTACCCTAACTAAGCAACAATa < 1:166615/90‑1 (MQ=255)
tatatTGACTCAA‑TTTCCAGCCTGGTTAAAAATAGCGACCAGCTCAGTCGCAAATATAGTGACTACCCTAACTAAGCAACAATAAGGAAt < 1:553718/90‑1 (MQ=255)
atatTGACTCAATTTCCCAGCCTGGTTAAAAATAGCGACCAGCTCAGTCGCAAATATAGTGACTACCCTAACTAAGCAACAATAAGGAAt < 2:131520/90‑1 (MQ=255)
atatTGACTCAATTTCCCAGCCTGGTTAAAAATAGCGACCAGCTCAGTCGCAAATATAGTGACTACCCTAACTAAGCAACAATAAGGAAt < 1:576282/90‑1 (MQ=255)
atatTGACTCAATTTCCCAGCCTGGTTAAAAATAGCGACCAGCTCAGTCGCAAATATAGTGACTACCCTAACTAAGCAACAATAAGGAAt < 1:204092/90‑1 (MQ=255)
gACTCAATTTCCCAGCCTGGTTAAAAATAGCGACCAGCTCAGTCGCAAATATAGTGACTACCCTAACTAAGCAACAATAAGGAATACACt > 2:567825/1‑90 (MQ=255)
aaTTTCCCAGCCTGGTTAAAAATAGCGACCAGCTCAGTCGCAAATATAGTGACTACCCTAACTAAGCAACAATAAGGAAt < 1:473960/80‑1 (MQ=255)
aaTTTCCCAGCCTGGTTAAAAATAGCGACCAGCTCAGTCGCAAATATAGTGACTACCCTAACTAAGCAACAATAAGGAAt > 2:473960/1‑80 (MQ=255)
|
GCGTGAATAATATTCAACACCAGTGCAGCATCATCATTACATACTTACAGCCGCCGACTACCGCTTTCGATATATTGACTCAATTTTCCAGCCTGGTTAAAAATAGCGACCAGCTCAGTCGCAAATATAGTGACTACCCTAACTAAGCAACAATAAGGAATACACT > NZ_CP009273/2029150‑2029315
|
| Alignment Legend |
|---|
Aligned base mismatch/match (shaded by quality score): ATCG/ATCG < 3 ≤ ATCG/ATCG < 22 ≤ 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
GGAAAATTTGGCGTGAATAATATTCAACACCAGTGCAGCATCATCATTACATACTTACAGCCGCCGACTACCGCTTTCGATATATTGACTCAATTTTCCAGCCTGGTTAAAAATAGCGACCAGCTCAGTCGCAAATATAGTGACTACCCTAACTAAGCAACAATAAGGAATACACTATGACTGTTCAAACAAGT > NZ_CP009273/2029140‑2029333
|
GGAAAATTTGGCGTGAATAATATTCAACACCAGTGCAGCATCATCATTACATACTTACAGCCGCCGACTACCGCTTTCGATATATTGACTCAATTTCCCA > SRR3722073.189155/1‑100 (MQ=60)
GAATAATATTCAACACCAGTGCAGCATCATCATTACATACTTACAGCCGCCGACTACCGCTTTCGATATATTGACTCAATTTCCCAGCCTGGTTAAAAAT > SRR3722073.28541/1‑100 (MQ=60)
TTCAACACCAGTGCAGCATCATCATTACATACTTACAGCCGCCGACTACCGCTTTCGATATATTGACTCAATTTCCCAGCCTGGTTAAAAATAGCGACCA > SRR3722073.170342/1‑100 (MQ=60)
GTGCAGCATCATCATTACATACTTACAGCCGCCGACTACCGCTTTCGATATATTGACTCAATTTCCCAGCCTGGTTAAAAATAGCGACCAGCTCAGTCGC > SRR3722073.392155/1‑100 (MQ=60)
TCATCATTACATACTTACAGCCGCCGACTACCGCTTTCGATATATTGACTCAATTTCCCAGCCTGGTTAAAAATAGCGACCAGCTCAGTCGCAAATATAG > SRR3722073.307268/1‑100 (MQ=60)
ATCATTACATACTTACAGCCGCCGACTACCGCTTTCGATATATTGACTCAATTTCCCAGCCTGGTTAAAAATAGCGACCAGCTCAGTCGCAAATATAGTG < SRR3722073.640233/100‑1 (MQ=60)
CATTACATACTTACAGCCGCCGACTACCGCTTTCGATATATTGACTCAATTTCCCAGCCTGGTTAAAAATAGCGACCAGCTCAGTCGCAAATATAGTGAC < SRR3722073.647966/100‑1 (MQ=60)
ACATACTTACAGCCGCCGACTACCGCTTTCGATATATTGACTCAATTTCCCAGCCTGGTTAAAAATAGCGACCAGCTCAGTCGCAAATATAGTGACTACC > SRR3722073.635553/1‑100 (MQ=60)
CATACTTACAGCCGCCGACTACCGCTTTCGATATATTGACTCAATTTCCCAGCCTGGTTAAAAATAGCGACCAGCTCAGTCGCAAATATAGTGACTACCC < SRR3722073.521313/100‑1 (MQ=60)
CATACTTACAACCGCCGACTACCGCTTTCGATATATTGACTCAATTTCCCAGCCTGGTTAAAAATAGCGACCAGCTCAGTCGCAAATATAGTGACTACCC < SRR3722073.515777/100‑1 (MQ=60)
TACTTACAGCCGCCGACTACCGCTTTCGATATATTGACTCAATTTCCCAGCCTGGTTAAAAATAGCGACCAGCTCAGTCGCAAATATAGTGACTACCCTA > SRR3722073.780932/1‑100 (MQ=60)
TACTTACAGCCGCCGACTACCGCTTTCGATATATTGACTCAATTTCCCAGCCTGGTTAAAAATAGCGACCAGCTCAGTCGCAAATATAGTGACTACCCTA > SRR3722073.134272/1‑100 (MQ=60)
CTTACAGCCGCCGACTACCGCTTTCGATATATTGACTCAATTTCCCAGCCTGGTTAAAAATAGCGACCAGCTCAGTCGCAAATATAGTGACTACCCTAAC < SRR3722073.362542/100‑1 (MQ=60)
CTTACAGCCGCCGACTACCGCTTTCGATATATTGACTCAATTTCCCAGCCTGGTTAAAAATAGCGACCAGCTCAGTCGCAAATATAGTGACTACCCTAAC < SRR3722073.550748/100‑1 (MQ=60)
CCGACTACCGCTTTCGATATATTGACTCAATTTCCCAGCCTGGTTAAAAATAGCGACCAGCTCAGTCGCAAATATAGTGACTACCCTAACTAAGCAACAA < SRR3722073.689321/100‑1 (MQ=60)
TACCGCTTTCGATATATTGACTCAATTTTCCAGCCTGGTTAAAAATAGCGACCAGCTCAGTCGCAAATATAGTGACTACCCTAACTAAGCAACAATAAGG < SRR3722073.387750/100‑1 (MQ=60)
TACCGCTTTCGATATATTGACTCAATTTCCCAGCCTGGTTAAAAATAGCGACCAGCTCAGTCGCAAATATAGTGACTACCCTAACTAAGCAACAATAAGG < SRR3722073.255715/100‑1 (MQ=60)
TACCGCTTTCGATATATTGACTCAATTTCCCAGCCTGGTTAAAAATAGCGACCAGCTCAGTCGCAAATATAGTGACTACCCTAACTAAGCAACAATAAGG < SRR3722073.624286/100‑1 (MQ=60)
TTCGATATATTGACTCAATTTCCCAGCCTGGTTAAAAATAGCGACCAGCTCAGTCGCAAATATAGTGACTACCCTAACTAAGCAACAATAAGGAATACAC < SRR3722073.190313/100‑1 (MQ=60)
TTCGATATATTGACTCAATTTCCCAGCCTGGTTAAAAATAGCGACCAGCTCAGTCGCAAATATAGTGACTACCCTAACTAAGCAACAATAAGGAATACAC < SRR3722073.169913/100‑1 (MQ=60)
TATATTGACTCAA‑TTTCCAGCCTGGTTAAAAATAGCGACCAGCTCAGTCGCAAATATAGTGACTACCCTAACTAAGCAACAATAAGGAATACACTATGAC < SRR3722073.565291/100‑1 (MQ=60)
ATATTGACTCAATTTCCCAGCCTGGTTAAAAATAGCGACCAGCTCAGTCGCAAATATAGTGACTACCCTAACTAAGCAACAATAAGGAATACACTATGAC < SRR3722073.484051/100‑1 (MQ=60)
ATATTGACTCAATTTCCCAGCCTGGTTAAAAATAGCGACCAGCTCAGTCGCAAATATAGTGACTACCCTAACTAAGCAACAATAAGGAATACACTATGAC < SRR3722073.588324/100‑1 (MQ=60)
ATATTGACTCAATTTCCCAGCCTGGTTAAAAATAGCGACCAGCTCAGTCGCAAATATAGTGACTACCCTAACTAAGCAACAATAAGGAATACACTATGAC < SRR3722073.208238/100‑1 (MQ=60)
GACTCAATTTCCCAGCCTGGTTAAAAATAGCGACCAGCTCAGTCGCAAATATAGTGACTACCCTAACTAAGCAACAATAAGGAATACACTATGACTGTTC > SRR3722073.292240/1‑100 (MQ=60)
TTCCCAGCCTGGTTAAAAATAGCGACCAGCTCAGTCGCAAATATAGTGACTACCCTAACTAAGCAACAATAAGGAATACACTATGACTGTTCAAACAAGT > SRR3722073.96442/1‑100 (MQ=60)
|
GGAAAATTTGGCGTGAATAATATTCAACACCAGTGCAGCATCATCATTACATACTTACAGCCGCCGACTACCGCTTTCGATATATTGACTCAATTTTCCAGCCTGGTTAAAAATAGCGACCAGCTCAGTCGCAAATATAGTGACTACCCTAACTAAGCAACAATAAGGAATACACTATGACTGTTCAAACAAGT > NZ_CP009273/2029140‑2029333
|
| Alignment Legend |
|---|
Aligned base mismatch/match (shaded by quality score): ATCG/ATCG < 0 ≤ ATCG/ATCG < 19 ≤ ATCG/ATCG < 29 ≤ ATCG/ATCG < 35 ≤ ATCG/ATCG < 41 ≤ ATCG/ATCG |
Unaligned base: atcg Masked matching base: atcg Alignment gap: ‑ Deleted base: ‑ |
