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 I200 R1
|
216 |
30.8 |
1683622 |
97.2% |
1636480 |
87.0 |
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 | 90.9%
| 82.9
/ 2.5
| 33 | E339G (GAA→GGA) | ggt | gamma‑glutamyltransferase |
| Reads supporting (aligned to +/- strand): ref base T (1/2); new base C (15/15); total (16/17) |
| Fisher's exact test for biased strand distribution p-value = 1.00e+00 |
| Kolmogorov-Smirnov test that lower quality scores support variant p-value = 9.08e-01 |
CAATTTGATCGGCAATAGATTTGGCATAGGCTTTATTGGTCAGCGCCTGCCACGGTACTTTGACAAAATCCGGGTCGCCAAGATAT‑TCCGAGCGGTCGGCGTAGGCGTATTTCTCCGCTTCTGCCATGATTTGCATCGCATCGGCGCTGCCAAAGCCGTATTTCTTC > NZ_CP009273/3579082‑3579248
|
cAATTTGATCGGCAATAGATTTGGCATAGGCTTTATTGGTCAGCGCCTGCCACGGTACTTTGACAAAATCCGGGTCGCCAAGATAT‑CCCg < 1:119847/90‑1 (MQ=255)
gATCGGCAATAGATTTGGCATAGGCTTTATTGGTCAGCGCCTGCCACGGTACTTTGACAAAATCCGGGTCGCCAAGATAT‑CCCGAGCGGt > 1:644871/1‑90 (MQ=255)
agcGGCAATAGATTTGGCATCGGCTTTACTGGGCCGCGCCTGCCACGGGACTATGACAAAATCCGGGTCGCCAAGATAT‑CCCGAGCGGTc < 2:783600/88‑1 (MQ=255)
accGGCAATAGATTTGGCATAGGCTTTCTTGGTCAGCGCCTGCCACGGTACTTTGCCAAAATCCGGGTCGCCAAGATAT‑CCCGAGCGGTc < 2:544987/88‑1 (MQ=255)
aTCGGCAATAGATTTGGCATAGGCTTTATTGGTCAGCGCCTGCCACGGTACTTTGACAAAATCCGGGTCGCCAAGATAT‑CCCGAGCGGTc < 1:526972/90‑1 (MQ=255)
aaTAGATTTGGCATAGGCTTTATTGGTCAGCGCCTGCCACGGTACTTTGACAAAATCCGGGTCGCCAAGATAT‑CCCGAGCGGTCggcgta < 1:758588/90‑1 (MQ=255)
tGGCATAGGCTTTATTGGTCAGCGCCTGCTACGGTACTTTGACAAAATCCGGGTCGCCAAGATAT‑CCCGAGCGGTCGGCGTAGGCGTAtt > 2:264963/1‑90 (MQ=255)
tGGCATAGGCTTTATTGGTCAGCGCCTGCCACGGTACTTTGACAAAATCCGGGTCGCCAAGATAT‑CCCGAGCGGTCGGCGTAGGCGTAtt > 1:88969/1‑90 (MQ=255)
tGGCATAGGCTTTATTGGTCAGCGCCTGCCACGGTACTTTGACAAAATCCGGGTCGCCAAGATAT‑CCCGAGCGGTCGGCGTAGGCGTAtt > 2:88592/1‑90 (MQ=255)
tGGCATAGGCTTTATTGGTCAGCGCCTGCCACGGTACTTTGACAAAATCCGGGTCGCCAAGATAT‑CCCGAGCGGTCGGCGTAGGCGTAtt > 2:21527/1‑90 (MQ=255)
tGGCATAGGCTTTATTGGTCAGCGCCTGCCACGGTACTTTGACAAAATCCGGGTCGCCAAGATAT‑CCCGAGCGGTCGGCGTAGGCGTAtt > 1:682749/1‑90 (MQ=255)
tGGCATAGGCTTTATTGGTCAGCGCCTGCCACGGTACTATGACAAAATCCGGGTCGCCAAGATAT‑CCCGAGCGGTCGGCGTAGGCGTAtt > 1:512063/1‑90 (MQ=255)
aTAGGCTTTATTGGTCAGCGCCTGCCACGGTACTTTGACAAAATCCGGGTCGCCAAGATAT‑CCCGAGCGGTCGGCGTAGGCGTATTtctc > 2:346723/1‑90 (MQ=255)
tAGGCTTTATTGGTCAGCGCCTGCCACGGTACTTTGACAAAATCCGGGTCGCCAAGATAT‑CCCGAGCGGTCGGCGTAGGCGTATTTCTcc < 1:531231/90‑1 (MQ=255)
tttATTGGTCAGCGCCTGCCACGGTACTTTGACAAAATCCGGGTCGCCAAGATAT‑CCCGAGCGGTCGGCGTAGGCGTATTTCTCCGCTTc < 1:399028/90‑1 (MQ=255)
aTTGGTCAGCGCCTGCCACGGTACTTTGACAAAATCCGGGTCGCCAAGATAT‑CCCGAGCGGTCGGCGTAGGCGTATTTCTCCGCTTCTGc < 2:512063/90‑1 (MQ=255)
tGGTCAGCGCCTGCCACGGTACTTTGACAAAATCCGGGTCGCCAAGATAT‑CCCGAGCGGTCGGCGTAGGCGTATTTCTCCGCTTCTGCCa < 2:301210/90‑1 (MQ=255)
ggTCAGCGCCTGCCACGGTACTTTGACAAAATCCGGGTCGCCAAGATAT‑CCCGAGCGGTCGGCGTAGGCGTATTTCTCCGCTTCTGCCAt > 1:482852/1‑90 (MQ=255)
tCAGCGCCTGCCACGGTACTTTGACAAAATCCGGGTCGCCAAGATAT‑CCCGAGCGGTCGGCGTAGGCGTATTTCTCCGCTTCTGCCATGa < 2:644871/90‑1 (MQ=255)
cAGCGCCTGCCACGGTACTTTGGCAAAATCCGGGTCGCCAAGATAT‑CCCGAGCGGTCGGCGTAGGCGTATTTCTCCGCTTCTGCCATGAt > 1:238363/1‑90 (MQ=255)
tGCCACGGTACTTTGACAAAATCCGGGTCGCCAAGATAT‑CCCGAGCGGTCGGCGTAGGCGTATTTCTCCGCTTCTGCCATGATTTgcatc > 2:73207/1‑90 (MQ=255)
aCTTTGACAAAATCCGGGTCGCCAAGATAT‑CCCGAGCGGTCGGGGTAGGCGTATTTCTCCGCTTCTGCCATGATTTGCATCGCATCGgcg < 2:521968/90‑1 (MQ=255)
aCTTTGACAAAATCCGGGTCGCCAAGATAT‑CCCGAGCGGTCGGCGTAGGCGTATTTCTCCGCTTCTGCCATGATTTGCATCGCATCGgcg < 2:174689/90‑1 (MQ=255)
cTTTGACAAAATCCGGGTCGCCAAGATAT‑CCCGAGCGGTCGGCGTAGGCGTATTTCTCCGCTTCTGCCATGATTTGCATCGCATCGgcgc > 1:549200/1‑90 (MQ=255)
gACAAAATCCGGGTCGCCAAGATAT‑CCCGAGCGGTCGGCGTAGGCGTATTTCTCCGCTTCTGCCATGATTTGCATCGCATCGGCGCTGcc > 1:707119/1‑90 (MQ=255)
aCAAAATCCGGGTCGCCAAGATAT‑CCCGAGCGGTCGGCGTAGGCGTATTTCTCCGCTTCTGCCATGATTTGCATCGCATCGGCGCTGCCa < 1:531772/90‑1 (MQ=255)
aaTCCGGGTCGCCAAGATAT‑TCCGAGCGGTCGGCGTAGGCGTATTTCTCCGCTTc < 1:828354/55‑1 (MQ=255)
aaTCCGGGTCGCCAAGATAT‑TCCGAGCGGTCGGCGTAGGCGTATTTCTCCGCTTc > 2:828354/1‑55 (MQ=255)
aaTCCGGGTCGCCAAGATAT‑TCCGAGCGGTCGGCGTAGGCGTATTTCTCCGCTTCTGCCATGATTTGCATCGCATCGGCGCTGCCAAAGc < 2:346186/90‑1 (MQ=255)
aaTCCGGGTCGCCAAGATAT‑CCCGAGCGGTCGGCGTAGGCGTATTTCTCCGCTTCTGCCATGATTTGCATCGCATCGGCGCTGCCAAAGc > 2:494425/1‑90 (MQ=255)
aaTCCGGGTCGCCAAGATAT‑CCCGAGCGGTCGGCGTAGGCGTATTTCTCCGCTTCTGCCATGATTTGCATCGCATCGGCGCTGCCAAAGc > 2:202777/1‑90 (MQ=255)
ccAAGATATCCCCGAGCGGTCGGCGTAGGCGTATTTCTCCGCTTCTGCCATGATTTGCATCGCATCGGCGCTGCCAAAGCCGTATttctt < 1:629014/90‑1 (MQ=255)
ccAAGATAT‑CCCGAGCGGTCGGCGTAGGCGTATTTCTCCGCTTCTGCCATGATTTGCATCGCATCGGCGCTGCCAAAGCCGTATttcttc < 1:734460/90‑1 (MQ=255)
|
CAATTTGATCGGCAATAGATTTGGCATAGGCTTTATTGGTCAGCGCCTGCCACGGTACTTTGACAAAATCCGGGTCGCCAAGATAT‑TCCGAGCGGTCGGCGTAGGCGTATTTCTCCGCTTCTGCCATGATTTGCATCGCATCGGCGCTGCCAAAGCCGTATTTCTTC > NZ_CP009273/3579082‑3579248
|
| Alignment Legend |
|---|
Aligned base mismatch/match (shaded by quality score): ATCG/ATCG < 3 ≤ ATCG/ATCG < 18 ≤ ATCG/ATCG < 29 ≤ 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
TTGATATCAATTTGATCGGCAATAGATTTGGCATAGGCTTTA‑TTGGTCAGCGCCTGCCACGGTACTTTGACAAAATCCGGGTCGCCAAGATAT‑TCCGAGCGGTCGGCGTAGGCGTATTTCTCCGCTTCTGCCATGATTTGCATCGCATCGGCGCTGCCAAAGCCGTATTTCTTCATATCGAAGT > NZ_CP009273/3579075‑3579258
|
TTGATATCAATTTGATCGGCAATAGATTTGGCATAGGCTTTATTTGGTCAGCGCCTGCCACGGTACTTTGACAAAATCCGGGTCGCCAAGATAT‑CCCGAG < SRR3722079.703949/100‑1 (MQ=60)
ATATCAATTTGATCGGCAATAGATTTGGCATAGGCTTTA‑TTGGTCAGCGCCTGCCACGGTACTTTGACAAAATCCGGGTCGCCAAGATAT‑CCCGAGCGGT > SRR3722079.651536/1‑100 (MQ=60)
CAATTTGATCGGCAATAGATTTGGCATAGGCTTTA‑TTGGTCAGCGCCTGCCACGGTACTTTGACAAAATCCGGGTCGCCAAGATAT‑CCCGAGCGGTCGGC < SRR3722079.120832/100‑1 (MQ=60)
ATCGGCAATAGATTTGGCATAGGCTTTA‑TTGGTCAGCGCCTGCCACGGTACTTTGACAAAATCCGGGTCGCCAAGATAT‑CCCGAGCGGTCGGCGTAGGCG < SRR3722079.531872/100‑1 (MQ=60)
GCAATAGATTTGGCATAGGCTTTA‑TTGGTCAGCGCCTGCCACGGTACTTTGACAAAATCCGGGTCGCCAAGATAT‑CCCGAGCGGTCGGCGTAGGCGTATT > SRR3722079.89674/1‑100 (MQ=60)
GCAATAGATTTGGCATAGGCTTTA‑TTGGTCAGCGCCTGCCACGGTACTTTGACAAAATCCGGGTCGCCAAGATAT‑CCCGAGCGGTCGGCGTAGGCGTATT > SRR3722079.689922/1‑100 (MQ=60)
GCAATAGATTTGGCATAGGCTTTA‑TTGGTCAGCGCCTGCCACGGTACTATGACAAAATCCGGGTCGCCAAGATAT‑CCCGAGCGGTCGGCGTAGGCGTATT > SRR3722079.516735/1‑100 (MQ=60)
AATAGATTTGGCATAGGCTTTA‑TTGGTCAGCGCCTGCCACGGTACTTTGACAAAATCCGGGTCGCCAAGATAT‑CCCGAGCGGTCGGCGTAGGCGTATTTC < SRR3722079.766705/100‑1 (MQ=60)
TAGGCTTTA‑TTGGTCAGCGCCTGCCACGGTACTTTGACAAAATCCGGGTCGCCAAGATAT‑CCCGAGCGGTCGGCGTAGGCGTATTTCTCCGCTTCTGCCA < SRR3722079.536185/100‑1 (MQ=60)
AGGCTTTA‑TTGGTCAGCGCCTGCCACGGTACTTTGACAAAATCCGGGTCGCCAAGATAT‑CCCGAGCGGTCGGCGTAGGCGTATTTCTCCGCTTCTGCCAT > SRR3722079.487071/1‑100 (MQ=60)
CTTTA‑TTGGTCAGCGCCTGCCACGGTACTTTGGCAAAATCCGGGTCGCCAAGATAT‑CCCGAGCGGTCGGCGTAGGCGTATTTCTCCGCTTCTGCCATGAT > SRR3722079.240369/1‑100 (MQ=60)
TTTA‑TTGGTCAGCGCCTGCCACGGTACTTTGACAAAATCCGGGTCGCCAAGATAT‑CCCGAGCGGTCGGCGTAGGCGTATTTCTCCGCTTCTGCCATGATT < SRR3722079.402380/100‑1 (MQ=60)
gctcggagatgtgtataagagacagACTTTGACAAAATCCGGGTCGCCAAGATAT‑TCCGAGCGGTCGGCGTAGGCGTATTTCTCCGCTTCTGCCATGATT < SRR3722079.837221/75‑1 (MQ=60)
TGCCACGGTACTTTGACAAAATCCGGGTCGCCAAGATAT‑CCCGAGCGGTCGGCGTAGGCGTATTTCTCCGCTTCTGCCATGATTTGCATCGCATCGGCGC > SRR3722079.554456/1‑100 (MQ=60)
ACGGTACTTTGACAAAATCCGGGTCGCCAAGATAT‑CCCGAGCGGTCGGCGTAGGCGTATTTCTCCGCTTCTGCCATGATTTGCATCGCATCGGCGCTGCC > SRR3722079.714625/1‑100 (MQ=60)
ACAAAATCCGGGTCGCCAAGATAT‑CCCGAGCGGTCGGCGTAGGCGTATTTCTCCGCTTCTGCCATGATTTGCATCGCATCGGCGCTGCCAAAGCCGTATT < SRR3722079.536732/100‑1 (MQ=60)
CCAAGATATCCCCGAGCGGTCGGCGTAGGCGTATTTCTCCGCTTCTGCCATGATTTGCATCGCATCGGCGCTGCCAAAGCCGTATTTCTTCATATCGAAG < SRR3722079.635430/100‑1 (MQ=60)
CCAAGATAT‑CCCGAGCGGTCGGCGTAGGCGTATTTCTCCGCTTCTGCCATGATTTGCATCGCATCGGCGCTGCCAAAGCCGTATTTCTTCATATCGAAGT < SRR3722079.742313/100‑1 (MQ=60)
|
TTGATATCAATTTGATCGGCAATAGATTTGGCATAGGCTTTA‑TTGGTCAGCGCCTGCCACGGTACTTTGACAAAATCCGGGTCGCCAAGATAT‑TCCGAGCGGTCGGCGTAGGCGTATTTCTCCGCTTCTGCCATGATTTGCATCGCATCGGCGCTGCCAAAGCCGTATTTCTTCATATCGAAGT > NZ_CP009273/3579075‑3579258
|
| Alignment Legend |
|---|
Aligned base mismatch/match (shaded by quality score): ATCG/ATCG < 0 ≤ ATCG/ATCG < 28 ≤ ATCG/ATCG < 34 ≤ ATCG/ATCG < 35 ≤ ATCG/ATCG < 41 ≤ ATCG/ATCG |
Unaligned base: atcg Masked matching base: atcg Alignment gap: ‑ Deleted base: ‑ |
