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 I227 R1
|
223 |
21.3 |
1167702 |
97.0% |
1132670 |
86.4 |
Breseq alignment
BRESEQ :: Evidence
|
| evidence |
seq id |
position |
mutation |
annotation |
gene |
description |
| RA |
NZ_CP009273 |
3,318,468 |
A→C |
A609A (GCT→GCG) |
ftsH ← |
ATP‑dependent zinc metalloprotease FtsH |
|
| |
seq id |
position |
ref |
new |
freq |
score (cons/poly) |
reads |
annotation |
genes |
product |
| * | NZ_CP009273 | 3,318,468 | 0 | A | C | 96.0%
| 72.7
/ ‑3.4
| 25 | A609A (GCT→GCG) | ftsH | ATP‑dependent zinc metalloprotease FtsH |
| Reads supporting (aligned to +/- strand): ref base A (1/0); new base C (14/10); total (15/10) |
| Fisher's exact test for biased strand distribution p-value = 1.00e+00 |
| Kolmogorov-Smirnov test that lower quality scores support variant p-value = 8.49e-01 |
GACATGGTGTTACCCGGGTTCGGCGTACGCGGTTCATCAACCGGACGAGGAGCCTTTGGACTACCATTGTCGCCAGAATTGTTAGAAGCGCCTGGTTCTTCCCAGCCCGCTGGCGGACGTACATCGCGACGTGCCATCAGGTCATCAATCTGCGGTGCGTCGATAGTCTCAT > NZ_CP009273/3318382‑3318553
|
gACATGGTGTTACCCGGGTTCGGCGTGCTCGGTTCATCAACCGGACGAGGAGCCTTTGGACTTCCATTGTCGCCAGAATTGTTAGAcgcg > 1:250518/1‑90 (MQ=255)
aTGGTGTTACCCGGGTTCGGCGTACGCGGTTCATCAACCGGACGAGGAGCCTTTGGACTACCATTGTCGCCAGAATTGTTAGACGCGCCt < 1:192292/90‑1 (MQ=255)
aTGGTGTTACCCGGGTTCGGCGTACGCGGTTCATCAACCGGACGAGGAGCCTTTGGACTACCATTGTCGCCAGAATTGTTAGACGCGCCt < 1:573669/90‑1 (MQ=255)
ggTGTTACCCGGGTTCGGCGTACGCGGTTCATCAACCGGACGAGGAGCCTTTGGACTACCATTGTCGCCAGAATTGTTAGACGCGCCTgg > 2:311304/1‑90 (MQ=255)
tACCCGGGTTCGGCGTACGCGGTTCATCAACCGGACGAGGAGCCTTTGGACTACCATTGTCGCCAGAATTGTTAGACGCGCCTGGttctt > 2:373415/1‑90 (MQ=255)
tACCCGGGTTCGGCGTACGCGGTTCATCAACCGGACGAGGAGCCTTTGGACTACCATTGTCGCCAGAATTGTTAGACGCGCCTGGttctt > 2:190361/1‑90 (MQ=255)
tACCCGGGTTCGGCGTACGCGGTTCATCAACCGGACGAGGAGCCTTTGGACTACCATTGTCGCCAGAATTGTTAGAAGCGCCTGGttctt > 1:352523/1‑90 (MQ=255)
ggTTCGGCGTACGCGGTTCATCAACCGGACGAGGAGCCTTTGGACTACCATTGTCGCCAGAATTGTTAGACGCGCCTGGTTCTTCCCAGc > 2:99491/1‑90 (MQ=255)
ggTTCGGCGTACGCGGTTCATCAACCGGACGAGGAGCCTTTGGACTACCATTGTCGCCAGAATTGTTAGACGCGCCTGGTTCTTCCCAGc > 2:350540/1‑90 (MQ=255)
cGGCGTACGCGGTTCATCAACCGGACGAGGAGCCTTTGGACTACCATTGTCGCCAGAATTGTTAGACGCGCCTGGTTCTTCCCAGCCCGc > 2:18710/1‑90 (MQ=255)
ttCATCAACCGGACGAGGAGCCTTTGGACTACCATTGTCGCCAGAATTGTTAGACGCGCCTGGTTCTTCCCAGCCCGCTGGCGGACGTAc > 2:166141/1‑90 (MQ=255)
catcaACCGGACGAGGAGCCTTTGGACTACCATTGTCGCCAGAATTGTTAGACGCGCCTGGTTCTTCCCAGCCCGCTGGCGGACGTACAt > 2:295816/1‑90 (MQ=255)
caACCGGACGAGGAGCCTTTGGACTACCATTGTCGCCAGAATTGTTAGACGCGCCTGGTTCTTCCCAGCCCGCTGGCGGACGTACATcgc > 2:185150/1‑90 (MQ=255)
cGGACGAGGAGCCTTTGGACTACCATTGTCGCCAGAATTTTTAGACGCGCCTGGTTCTTCCCAGCCCGCTGGCGGACGTGCATCGCGACg > 1:66390/1‑90 (MQ=255)
cGGACGAGGAGCCTTTGGACTACCATTGTCGCCAGAATTGTTAGACGCGCCTGGTTCTTCCCAGCCCGCTGGCGGACGTACATCGCGACg < 1:373415/90‑1 (MQ=255)
cGGACGAGGAGCCTTTGGACTACCATTGTCGCCAGAATTGTTAGACGCGCCTGGTTCTTCCCAGCCCGCTGGCGGACGTACATCGCGACg > 2:393699/1‑90 (MQ=255)
gaggagCCTTTGGACTACCATTGTCGCCAGAATTGTTAGACGCGCCTGGTTCTTCCCAGCCCGCTGGCGGACGTACATCGCGACGTGCCa < 1:250885/90‑1 (MQ=255)
ggagCCTTTGGACTACCATTGTCGCCAGAATTGTTAGACGCGCCTGGTTCTTCCCAGCCCGCTGGCGGACGTACATCGCGACGTGCCATc < 2:346779/90‑1 (MQ=255)
ggagCCTTTGGACTACCATTGTCGCCAGAATTGTTAGACGCGCCTGGTTCTTCCCAGCCCGCTGGCGGACGTACATCGCGACGTGCCATc < 1:311304/90‑1 (MQ=255)
cTTTGGACTACCATTGTCGCCAGAATTGTTAGACGCGCCTGGTTCTTCCCAGCCCGCTGGCGGACGTACATCGCGACGTGCCATCAGGtc > 2:566635/1‑90 (MQ=255)
gTCGCCAGAATTGTTAGACGCGCCTGGTTCTTCCCAGCCCGCTGGCGGACGTACATCGCGACGTGCCATCAGGTCATCAATCTGCGGTGc > 1:360238/1‑90 (MQ=255)
cGCCAGAATTGTTAGACGCGCCTGGTTCTTCCCAGCCCGCTGGCGGACGTACATCGCGACGTGCCATCAGGTCATCAATCTGCGGTGCGt > 2:536330/1‑90 (MQ=255)
aGAATTGTTAGACGCGCCTGGTTCTTCCCAGCCCGCTGGCGGACGTACATCGCGACGTGCCATCAGGTCATCAATCTGCGGTGCGTCGAt < 1:315204/90‑1 (MQ=255)
gTTAGACGCGCCTGGTTCTTCCCAGCCCGCTGGCGGACGTACATCGCGACGTGCCATCAGGTCATCAATCTGCGGTGCGTCGATAGtctc < 1:349756/90‑1 (MQ=255)
tAGACGCGCCTGGTTCTTCCCAGCCCGCTGGCGGACGTACATCGCGACGTGCCATCAGGTCATCAATCTGCGGTGCGTCGATAGTCTCat < 2:505097/90‑1 (MQ=255)
tAGACGCGCCTGGTTCTTCCCAGCCCGCTGGCGGACGTACATCGCGACGTGCCATCAGGTCATCAATCTGCGGTGCGTCGATAGTCTCat < 2:505098/90‑1 (MQ=255)
|
GACATGGTGTTACCCGGGTTCGGCGTACGCGGTTCATCAACCGGACGAGGAGCCTTTGGACTACCATTGTCGCCAGAATTGTTAGAAGCGCCTGGTTCTTCCCAGCCCGCTGGCGGACGTACATCGCGACGTGCCATCAGGTCATCAATCTGCGGTGCGTCGATAGTCTCAT > NZ_CP009273/3318382‑3318553
|
| Alignment Legend |
|---|
Aligned base mismatch/match (shaded by quality score): ATCG/ATCG < 3 ≤ ATCG/ATCG < 17 ≤ 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
TAACTGCTCTGACATGGTGTTACCCGGGTTCGGCGTACGCGGTTCATCAACCGGACGAGGAGCCTTTGGACTACCATTGTCGCCAGAATTGTTAGAAGCGCCTGGTTCTTCCCAGCCCGCTGGCGGACGTACATCGCGACGTGCCATCAGGTCATCAATCTGCGGTGCGTCGATAGTCTCATATTTCATGAGAGC > NZ_CP009273/3318372‑3318566
|
TAACTGCTCTGACATGGTGTTACCCGGGTTCGGCGTGCTCGGTTCATCAACCGGACGAGGAGCCTTTGGACTTCCATTGTCGCCAGAATTGTTAGACGCG > SRR3722111.253464/1‑100 (MQ=60)
GACATGGTGTTACCCGGGTTCGGCGTACGCGGTTCATCAACCGGACGAGGAGCCTTTGGACTACCATTGTCGCCAGAATTGTTAGAAGCGCCTGGTTCTT > SRR3722111.357338/1‑100 (MQ=60)
ATGGTGTTACCCGGGTTCGGCGTACGCGGTTCATCAACCGGACGAGGAGCCTTTGGACTACCATTGTCGCCAGAATTGTTAGACGCGCCTGGTTCTTCCC < SRR3722111.194693/100‑1 (MQ=60)
ATGGTGTTACCCGGGTTCGGCGTACGCGGTTCATCAACCGGACGAGGAGCCTTTGGACTACCATTGTCGCCAGAATTGTTAGACGCGCCTGGTTCTTCCC < SRR3722111.582672/100‑1 (MQ=60)
GTTCATCAACCGGACGAGGAGCCTTTGGACTACCATTGTCGCCAGAATTTTTAGACGCGCCTGGTTCTTCCCAGCCCGCTGGCGGACGTGCATCGCGACG > SRR3722111.67174/1‑100 (MQ=60)
CGGACGAGGAGCCTTTGGACTACCATTGTCGCCAGAATTGTTAGACGCGCCTGGTTCTTCCCAGCCCGCTGGCGGACGTACATCGCGACGTGCCATCAGG < SRR3722111.378715/100‑1 (MQ=60)
GAGGAGCCTTTGGACTACCATTGTCGCCAGAATTGTTAGACGCGCCTGGTTCTTCCCAGCCCGCTGGCGGACGTACATCGCGACGTGCCATCAGGTCATC < SRR3722111.253835/100‑1 (MQ=60)
GGAGCCTTTGGACTACCATTGTCGCCAGAATTGTTAGACGCGCCTGGTTCTTCCCAGCCCGCTGGCGGACGTACATCGCGACGTGCCATCAGGTCATCAA < SRR3722111.315390/100‑1 (MQ=60)
GACTACCATTGTCGCCAGAATTGTTAGACGCGCCTGGTTCTTCCCAGCCCGCTGGCGGACGTACATCGCGACGTGCCATCAGGTCATCAATCTGCGGTGC > SRR3722111.365226/1‑100 (MQ=60)
AGAATTGTTAGACGCGCCTGGTTCTTCCCAGCCCGCTGGCGGACGTACATCGCGACGTGCCATCAGGTCATCAATCTGCGGTGCGTCGATAGTCTCATAT < SRR3722111.319348/100‑1 (MQ=60)
GTTAGACGCGCCTGGTTCTTCCCAGCCCGCTGGCGGACGTACATCGCctgtctcttatacacatctgacgctgccgacgaatgtcaatgtgtagatctcg > SRR3722111.532725/1‑47 (MQ=60)
GTTAGACGCGCCTGGTTCTTCCCAGCCCGCTGGCGGACGTACATCGCGACGTGCCATCAGGTCATCAATCTGCGGTGCGTCGATAGTCTCATATTTCATG < SRR3722111.354497/100‑1 (MQ=60)
ACGCGCCTGGTTCTTCCCGGCCCGCTGGCGGACGTACATCGCGACGTGCCATCAGGTCAACAATCTGCGGTGCGTCGATAGTCTCATATTTCATGAGAGC < SRR3722111.533693/100‑1 (MQ=60)
|
TAACTGCTCTGACATGGTGTTACCCGGGTTCGGCGTACGCGGTTCATCAACCGGACGAGGAGCCTTTGGACTACCATTGTCGCCAGAATTGTTAGAAGCGCCTGGTTCTTCCCAGCCCGCTGGCGGACGTACATCGCGACGTGCCATCAGGTCATCAATCTGCGGTGCGTCGATAGTCTCATATTTCATGAGAGC > NZ_CP009273/3318372‑3318566
|
| Alignment Legend |
|---|
Aligned base mismatch/match (shaded by quality score): ATCG/ATCG < 0 ≤ ATCG/ATCG < 10 ≤ ATCG/ATCG < 23 ≤ ATCG/ATCG < 33 ≤ ATCG/ATCG < 41 ≤ ATCG/ATCG |
Unaligned base: atcg Masked matching base: atcg Alignment gap: ‑ Deleted base: ‑ |
