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 I207 R1
|
218 |
45.0 |
2482936 |
97.1% |
2410930 |
86.1 |
Breseq alignment
BRESEQ :: Evidence
|
| evidence |
seq id |
position |
mutation |
annotation |
gene |
description |
| RA |
NZ_CP009273 |
3,579,168 |
T→C |
E339G (GAA→GGA) |
ggt ← |
gamma‑glutamyltransferase |
|
| |
seq id |
position |
ref |
new |
freq |
score (cons/poly) |
reads |
annotation |
genes |
product |
| * | NZ_CP009273 | 3,579,168 | 0 | T | C | 100.0%
| 164.5
/ NA
| 47 | E339G (GAA→GGA) | ggt | gamma‑glutamyltransferase |
| Reads supporting (aligned to +/- strand): ref base T (0/0); new base C (27/20); total (27/20) |
TGATCGGCAATAGATTTGGCATAGGCTTTATTGGTCAGCGCCTGCCACGGTACTTTGACAAAATCCGGGTCGCCAAGATATTCCGAGCGGTCGGCGTAGGCGTATTTCTCCGCTTCTGCCATGATTTGCATCGCATCGGCGCTGCCAAAGCCGTATTTCTTCATATC > NZ_CP009273/3579087‑3579253
|
tGATCGGCAATAGATTTGGCATAGGCTTTATTGGTCAGCGCCTGCCACGGTACTTTGACAAAATCCGGGTCGCCAAGATATCCCGAGCgg > 2:156182/1‑90 (MQ=255)
gATCGGCAATAGATTTAGCATAGGCTTTATTGGTCAGCGCCTGCCACGGTACTTTGACAAAATCCGGGTCGCCAAGATATCCCGAGCGGt > 1:19750/1‑90 (MQ=255)
aTCGGCAATAGATTTGGCATAGGCTTTATTGGTCAGCGCCTGCCACGGTACTTTGACAAAATCCGGGTCGCCAAGATATCCCGAGCGGTc < 1:1154499/90‑1 (MQ=255)
aTCGGCAATAGATTTGGCATAGGCTTTATTGGTCAGCGCCTGCCACGGTACTTTGACAAAATCCGGGTCGCCAAGATATCCCGAGCGGTc < 1:123498/90‑1 (MQ=255)
aTCGGCAATAGATTTGGCATAGGCTTTATTGGTCAGCGCCTGCCACGGTACTTTGACAAAATCCGGGTCGCCAAGATATCCCGAGCGGTc < 1:1221373/90‑1 (MQ=255)
cAATAGATTTGGCATAGGCTTTATTGGTCAGCGCCTGCCACGGTACTTTGACAAAATCCGGGTCGCCAAGATATCCCGAGCGGTCggcgt < 1:393978/90‑1 (MQ=255)
tAGATTTGGCATAGGCTTTATTGGTCAGCGCCTGCCACGGTACTTTGACAAAATCCGGGTCGCCAAGATATCCCGAGCGGTCggcgtagg < 1:283910/90‑1 (MQ=255)
ttGGCATAGGCTTTATTGGTCAGCGCCTGCCACGGTACTTTGACAAAATCCGGGTCGCCAAGATATCCCGAGCGGTCGGCGTAGGCGTAt > 2:1003775/1‑90 (MQ=255)
tGGCATAGGCTTTATTGGTCAGCGCCTGCCACGGTACTTTGACAAAATCCGGGTCGCCAAGATATCCCGAGCGGTCGGCGTAGGCGTAtt > 1:115550/1‑90 (MQ=255)
tGGCATAGGCTTTATTGGTCAGCGCCTGCCACGGTACTTTGACAAAATCCGGGTCGCCAAGATATCCCGAGCGGTCGGCGTAGGCGTAtt > 2:131803/1‑90 (MQ=255)
tGGCATAGGCTTTATTGGTCAGCGCCTGCCACGGTACTTTGACAAAATCCGGGTCGCCAAGATATCCCGAGCGGTCGGCGTAGGCGTAtt > 1:312215/1‑90 (MQ=255)
tGGCATAGGCTTTATTGGTCAGCGCCTGCCACGGTACTTTGACAAAATCCGGGTCGCCAAGATATCCCGAGCGGTCGGCGTAGGCGTAtt > 1:348942/1‑90 (MQ=255)
tGGCATAGGCTTTATTGGTCAGCGCCTGCCACGGTACTTTGACAAAATCCGGGTCGCCAAGATATCCCGAGCGGTCGGCGTAGGCGTAtt > 1:740853/1‑90 (MQ=255)
aTAGGCTTTATTGGTCAGCGCCTGCCACGGTACTTTGACAAAATCCGGGTCGCCAAGATATCCCGAGCGGTCGGCGTAGGCGTATTtctc < 2:734164/90‑1 (MQ=255)
tttATTGGTCAGCGCCTGCCACGGTACTTTGACAAAATCCGGGTCGCCAAGATATCCCGAGCGGTCGGCGTAGGCGTATTTCTCCGCTTc < 1:1003775/90‑1 (MQ=255)
tttATTGGTCAGCGCCTGCCACGGTACTTTGACAAAATCCGGGTCGCCAAGATATCCCGAGCGGTCGGCGTAGGCGTATTTCTCCGCTTc < 2:1193230/90‑1 (MQ=255)
ttATTGGTCAGCGCCTGCCACGGTACTTTGACAAAATCCGGGTCGCCAAGATATCCCGAGCGGTCGGCGTAGGCGTATTTCTCCGCTTCt > 2:30238/1‑90 (MQ=255)
ttATTGGTCAGCGCCTGCCACGGTACTTTGACAAAATCCGGGTCGCCAAGATATCCCGAGCGGTCGGCGTAGGCGTATTTCTCCGCTTCt > 2:100021/1‑90 (MQ=255)
tATTGGTCAGCGCCTGCCACGGTACTTTGACAAAATCCGGGTCGCCAAGATATCCCGAGCGGTCGGCGTAGGCGTATTTCTCCGCTTCTg > 2:1170614/1‑90 (MQ=255)
tGGTCAGCGCCTGCCACGGTACTTTGACAAAATCCGGGTCGCCAAGATATCCCGAGCGGTCGGCGTAGGCGTATTTCTCCGCTTCTGCCa < 2:90295/90‑1 (MQ=255)
tGGTCAGCGCCTGCCACGGTACTTTGACAAAATCCGGGTCGCCAAGATATCCCGAGCGGTCGGCGTAGGCGTATTTCTCCGCTTCTGCCa < 1:48185/90‑1 (MQ=255)
gTCAGCGCCTGCCACGGTACTTTGACAAAATCCGGGTCGCCAAGATATCCCGAGCGGTCGGCGTAGGCGTATTTCTCCGCTTCTGCCATg > 2:597002/1‑90 (MQ=255)
gTCAGCGCCTGCCACGGTACTTTGACAAAATCCGGGTCGCCAAGATATCCCGAGCGGTCGGCGTAGGCGTATTTCTCCGCTTCTGCCATg > 2:1170484/1‑90 (MQ=255)
gTCAGCGCCTGCCACGGTACTTTGACAAAATCCGGGTCGCCAAGATATCCCGAGCGGTCGGCGTAGGCGTATTTCTCCGCTTCTGCCATg > 1:168731/1‑90 (MQ=255)
gTCAGCGCCTGCCACGGTACTTTGACAAAATCCGGGTCGCCAAGATATCCCGAGCGGTCGGCGTAGGCGTATTTCTCCGCTTCTGCCATg > 1:181430/1‑90 (MQ=255)
cAGCGCCTGCCACGGTACTTTGACAAAATCCGGGTCGCCAAGATATCCCGAGCGGTc < 1:487660/57‑1 (MQ=255)
cAGCGCCTGCCACGGTACTTTGACAAAATCCGGGTCGCCAAGATATCCCGAGCGGTc > 2:487660/1‑57 (MQ=255)
cAGCGCCTGCCACGGTACTTTGACAAAATCCGGGTCGCCAAGATATCCCGAGCGGTCGGCGTAGGCGTATTTCTCCGCTTCTGCCATGAt > 2:387400/1‑90 (MQ=255)
aGCGCCTGCCACGGTACTTTGACAAAATCCGGGTCGCCAAGATATCCCGAGCGGTCGGCGTAGGCGTATTTCTCCGCTTCTGCCATGAtt < 2:281978/90‑1 (MQ=255)
gcgcCTGCCACGGTACTTTGACAAAATCCGGGTCGCCAAGATATCCCGAGCGGTCGGCGTAGGCGTATTTCTCCGCTTCTGCCa < 2:202844/84‑1 (MQ=255)
gcgcCTGCCACGGTACTTTGACAAAATCCGGGTCGCCAAGATATCCCGAGCGGTCGGCGTAGGCGTATTTCTCCGCTTCTGCCa > 1:202844/1‑84 (MQ=255)
gcgcCTGCCACGGTACTTTGACAAAATCCGGGTCGCCAAGATATCCCGAGCGGTCGGCGTAGGCGTATTTCTCCGCTTCTGCCATGAttt > 1:598136/1‑90 (MQ=255)
tGCCACGGTACTTTGACAAAATCCGGGTCGCCAAGATATCCCGAGc < 1:523159/46‑1 (MQ=255)
tGCCACGGTACTTTGACAAAATCCGGGTCGCCAAGATATCCCGAGc > 2:523159/1‑46 (MQ=255)
tGCCACGGTACTTTGACAAAATCCGGGTCGCCAAGATATCCCGAGCGGTCGGCGTAGGCGTATTTCTCCGCTTCTGCCATGATTTgcatc > 1:474703/1‑90 (MQ=255)
cGGTACTTTGACAAAATCCGGGTCGCCAAGATATCCCGAGCGGTCGGCGTAGGCGTATTTCTCCGCTTCTGCCATGATTTgcatcgcatc > 1:1221120/1‑90 (MQ=255)
ttGACAAAATCCGGGTCGCCAAGATATCCCGAGCGGTCGGCGTAGGCGTATTTCTCCGCTTCTGCCATGATTTgcat < 2:1214499/77‑1 (MQ=255)
ttGACAAAATCCGGGTCGCCAAGATATCCCGAGCGGTCGGCGTAGGCGTATTTCTCCGCTTCTGCCATGATTTgcat > 1:1214499/1‑77 (MQ=255)
ttGACAAAATCCGGGTCGCCAAGATATCCCGAGCGGTCGGCGTAGGCGTATTTCTCCGCTTCTGCCATGATTTGCATCGCGTCGGCGCTg > 2:889811/1‑90 (MQ=255)
aCAAAATCCGGGTCGCCAAGATATCCCGAGCGGTCGGCGTAGGCGTATTTCTCCGCTTCTGCCATGATTTGCATCGCATCGGCGCTGCCa > 2:1069401/1‑90 (MQ=255)
aaaaTCCGGGTCGCCAAGATATCCCGAGCGGTCGGCGTAGGCGTATTTCTCCGCTTCTGCCATGATTTGCATCGCATCGGCGCTGCCaaa > 2:525788/1‑90 (MQ=255)
aaTCCGGGTCGCCAAGATATCCCGAGCGGTCGGCGTAGGCGTATTTCTCCGCTTCTGCCATGATTTGCATCGCATCGGCGCTGCCAAAGc < 1:159546/90‑1 (MQ=255)
aTCCGGGTCGCCAAGATATCCCGAGCGGTCGGCGTAGGCGTATTTCTCCGCTTCTGCCATGATTTGCATCGCATCGGCGCTGCCAAAGcc < 1:287573/90‑1 (MQ=255)
gggTCGCCAAGATATCCCGAGCGGTCGGCGTAGGCGTATTTCTCCGCTTCTGCCATGATTTGCATCGCATCGGCGCTGCCAAAGCCGTAt > 1:633547/1‑90 (MQ=255)
ccAAGATATCCCGAGCGGTCGGCGTAGGCGTATTTCTCCGCTTCTGCCATGATTTGCATCGCATCGGCGCTGCCAAAGCCGTATttcttc < 1:387400/90‑1 (MQ=255)
atatCCCGAGCGGTCGGCGTAGGCGTATTTCTCCGCTTCTGCCATGATTTGCATCGCATCGGCGCTGCCAAAGCCGTATTTCTTCATATc < 1:552973/90‑1 (MQ=255)
atatCCCGAGCGGTCGGCGTAGGCGTATTTCTCCGCTTCTGCCATGATTTGCATCGCATCGGCGCTGCCAAAGCCGTATTTCTTCATATc < 2:715080/90‑1 (MQ=255)
|
TGATCGGCAATAGATTTGGCATAGGCTTTATTGGTCAGCGCCTGCCACGGTACTTTGACAAAATCCGGGTCGCCAAGATATTCCGAGCGGTCGGCGTAGGCGTATTTCTCCGCTTCTGCCATGATTTGCATCGCATCGGCGCTGCCAAAGCCGTATTTCTTCATATC > NZ_CP009273/3579087‑3579253
|
| Alignment Legend |
|---|
Aligned base mismatch/match (shaded by quality score): ATCG/ATCG < 3 ≤ ATCG/ATCG < 33 ≤ ATCG/ATCG < 35 ≤ 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
ATATCAATTTGATCGGCAATAGATTTGGCATAGGCTTTATTGGTCAGCGCCTGCCACGGTACTTTGACAAAATCCGGGTCGCCAAGATATTCCGAGCGGTCGGCGTAGGCGTATTTCTCCGCTTCTGCCATGATTTGCATCGCATCGGCGCTGCCAAAGCCGTATTTCTTCATATCGAAGTTTTCC > NZ_CP009273/3579078‑3579263
|
ATATCAATTTGATCGGCAATAGATTTAGCATAGGCTTTATTGGTCAGCGCCTGCCACGGTACTTTGACAAAATCCGGGTCGCCAAGATATCCCGAGCGGT > SRR3722089.19993/1‑100 (MQ=60)
gtcgtcggcagcgtcagatgtgtataagagacagGGTCAGCGCCTGCCACGGTACTTTGACAAAATCCGGGTCGCCAAGATATCCCGAGCGGTCGGCGTA < SRR3722089.529276/66‑1 (MQ=60)
cgtcagatgtgtataagagacaGCTTTATTGGTCAGCGCCTGCCACGGTACTTTGACAAAATCCGGGTCGCCAAGATATCCCGAGCGGTCGGCGTAGGCG < SRR3722089.493451/78‑1 (MQ=60)
ATCGGCAATAGATTTGGCATAGGCTTTATTGGTCAGCGCCTGCCACGGTACTTTGACAAAATCCGGGTCGCCAAGATATCCCGAGCGGTCGGCGTAGGCG < SRR3722089.1172068/100‑1 (MQ=60)
ATCGGCAATAGATTTGGCATAGGCTTTATTGGTCAGCGCCTGCCACGGTACTTTGACAAAATCCGGGTCGCCAAGATATCCCGAGCGGTCGGCGTAGGCG < SRR3722089.1239940/100‑1 (MQ=60)
ATCGGCAATAGATTTGGCATAGGCTTTATTGGTCAGCGCCTGCCACGGTACTTTGACAAAATCCGGGTCGCCAAGATATCCCGAGCGGTCGGCGTAGGCG < SRR3722089.125005/100‑1 (MQ=60)
GCAATAGATTTGGCATAGGCTTTATTGGTCAGCGCCTGCCACGGTACTTTGACAAAATCCGGGTCGCCAAGATATCCCGAGCGGTCGGCGTAGGCGTATT > SRR3722089.116962/1‑100 (MQ=60)
GCAATAGATTTGGCATAGGCTTTATTGGTCAGCGCCTGCCACGGTACTTTGACAAAATCCGGGTCGCCAAGATATCCCGAGCGGTCGGCGTAGGCGTATT > SRR3722089.353276/1‑100 (MQ=60)
GCAATAGATTTGGCATAGGCTTTATTGGTCAGCGCCTGCCACGGTACTTTGACAAAATCCGGGTCGCCAAGATATCCCGAGCGGTCGGCGTAGGCGTATT > SRR3722089.750562/1‑100 (MQ=60)
GCAATAGATTTGGCATAGGCTTTATTGGTCAGCGCCTGCCACGGTACTTTGACAAAATCCGGGTCGCCAAGATATCCCGAGCGGTCGGCGTAGGCGTATT > SRR3722089.316172/1‑100 (MQ=60)
CAATAGATTTGGCATAGGCTTTATTGGTCAGCGCCTGCCACGGTACTTTGACAAAATCCGGGTCGCCAAGATATCCCGAGCGGTCGGCGTAGGCGTATTT < SRR3722089.398780/100‑1 (MQ=60)
TAGATTTGGCATAGGCTTTATTGGTCAGCGCCTGCCACGGTACTTTGACAAAATCCGGGTCGCCAAGATATCCCGAGCGGTCGGCGTAGGCGTATTTCTC < SRR3722089.287545/100‑1 (MQ=60)
GGCTTTATTGGTCAGCGCCTGCCACGGTACTTTGACAAAATCCGGGTCGCCAAGATATCCCGAGCGGTCGGCGTAGGCGTATTTCTCCGCTTCTGCCATG > SRR3722089.170846/1‑100 (MQ=60)
GGCTTTATTGGTCAGCGCCTGCCACGGTACTTTGACAAAATCCGGGTCGCCAAGATATCCCGAGCGGTCGGCGTAGGCGTATTTCTCCGCTTCTGCCATG > SRR3722089.183694/1‑100 (MQ=60)
TTTATTGGTCAGCGCCTGCCACGGTACTTTGACAAAATCCGGGTCGCCAAGATATCCCGAGCGGTCGGCGTAGGCGTATTTCTCCGCTTCTGCCATGATT < SRR3722089.1018712/100‑1 (MQ=60)
TTATTGGTCAGCGCCTGCCACGGTACTTTGACAAAATCCGGGTCGCCAAGATATCCCGAGCGGTCGGCGTAGGCGTATTTCTCCGCTTCTGCCATGATTT > SRR3722089.205403/1‑100 (MQ=60)
TTATTGGTCAGCGCCTGCCACGGTACTTTGACAAAATCCGGGTCGCCAAGATATCCCGAGCGGTCGGCGTAGGCGTATTTCTCCGCTTCTGCCATGATTT > SRR3722089.605463/1‑100 (MQ=60)
TGGTCAGCGCCTGCCACGGTACTTTGACAAAATCCGGGTCGCCAAGATATCCCGAGCGGTCGGCGTAGGCGTATTTCTCCGCTTCTGCCATGATTTGCAT < SRR3722089.48788/100‑1 (MQ=60)
GGTCAGCGCCTGCCACGGTACTTTGACAAAATCCGGGTCGCCAAGATATCCCGAGCGGTCGGCGTAGGCGTATTTCTCCGCTTCTGCCATGATTTGCATC > SRR3722089.480361/1‑100 (MQ=60)
GCGCCTGCCACGGTACTTTGACAAAATCCGGGTCGCCAAGATATCCCGAGCGGTCGGCGTAGGCGTATTTCTCCGCTTCTGCCATGATTTGCATCGCATC > SRR3722089.1239686/1‑100 (MQ=60)
CCACGGTACTTTGACAAAATCCGGGTCGCCAAGATATCCCGAGCGGTCGGCGTAGGCGTATTTCTCCGCTTCTGCCATGATTTGCATCGCATCGGCGCTG > SRR3722089.1232978/1‑100 (MQ=60)
cgtcagatgtgtataagagacagCGCCAAGATATCCCGAGCGGTCGGCGTAGGCGTATTTCTCCGCTTCTGCCATGATTTGCATCGCATCGGCGCTGCCA < SRR3722089.1137457/77‑1 (MQ=60)
cgtcagatgtgtataagagacagAAGATATCCCGAGCGGTCGGCGTAGGCGTATTTCTCCGCTTCTGCCATGATTTGCATCGCATCGGCGCTGCCAAAGC < SRR3722089.803849/77‑1 (MQ=60)
GACAAAATCCGGGTCGCCAAGATATCCCGAGCGGTCGGCGTAGGCGTATTTCTCCGCTTCTGCCATGATTTGCATCGCATCGGCGCTGCCAAAGCCGTAT > SRR3722089.641607/1‑100 (MQ=60)
AATCCGGGTCGCCAAGATATCCCGAGCGGTCGGCGTAGGCGTATTTCTCCGCTTCTGCCATGATTTGCATCGCATCGGCGCTGCCAAAGCCGTATTTCTT < SRR3722089.161526/100‑1 (MQ=60)
ATCCGGGTCGCCAAGATATCCCGAGCGGTCGGCGTAGGCGTATTTCTCCGCTTCTGCCATGATTTGCATCGCATCGGCGCTGCCAAAGCCGTATTTCTTC < SRR3722089.291252/100‑1 (MQ=60)
CGCCAAGATATCCCGAGCGGTCGGCGTAGGCGTATTTCTCCGCTTCTGCCATGATTTGCATCGCATCGGCGCTGCCAAAGCCGTATTTCTTCATATCGAA > SRR3722089.161157/1‑100 (MQ=60)
CCAAGATATCCCGAGCGGTCGGCGTAGGCGTATTTCTCCGCTTCTGCCATGATTTGCATCGCATCGGCGCTGCCAAAGCCGTATTTCTTCATATCGAAGT < SRR3722089.392120/100‑1 (MQ=60)
ATATCCCGAGCGGTCGGCGTAGGCGTATTTCTCCGCTTCTGCCATGATTTGCATCGCATCGGCGCTGCCAAAGCCGTATTTCTTCATATCGAAGTTTTCC < SRR3722089.559397/100‑1 (MQ=60)
|
ATATCAATTTGATCGGCAATAGATTTGGCATAGGCTTTATTGGTCAGCGCCTGCCACGGTACTTTGACAAAATCCGGGTCGCCAAGATATTCCGAGCGGTCGGCGTAGGCGTATTTCTCCGCTTCTGCCATGATTTGCATCGCATCGGCGCTGCCAAAGCCGTATTTCTTCATATCGAAGTTTTCC > NZ_CP009273/3579078‑3579263
|
| Alignment Legend |
|---|
Aligned base mismatch/match (shaded by quality score): ATCG/ATCG < 0 ≤ ATCG/ATCG < 33 ≤ ATCG/ATCG < 34 ≤ ATCG/ATCG < 35 ≤ ATCG/ATCG < 41 ≤ ATCG/ATCG |
Unaligned base: atcg Masked matching base: atcg Alignment gap: ‑ Deleted base: ‑ |
