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 I194 R1
|
197 |
32.2 |
1845014 |
95.2% |
1756453 |
85.4 |
Breseq alignment
BRESEQ :: Evidence
|
| evidence |
seq id |
position |
mutation |
annotation |
gene |
description |
| RA |
NZ_CP009273 |
4,421,635 |
C→G |
A56P (GCA→CCA) |
ytfE ← |
iron‑sulfur cluster repair protein YtfE |
|
| |
seq id |
position |
ref |
new |
freq |
score (cons/poly) |
reads |
annotation |
genes |
product |
| * | NZ_CP009273 | 4,421,635 | 0 | C | G | 93.0%
| 133.6
/ 0.3
| 43 | A56P (GCA→CCA) | ytfE | iron‑sulfur cluster repair protein YtfE |
| Reads supporting (aligned to +/- strand): ref base C (1/2); new base G (12/28); total (13/30) |
| Fisher's exact test for biased strand distribution p-value = 1.00e+00 |
| Kolmogorov-Smirnov test that lower quality scores support variant p-value = 6.22e-01 |
TGGTAGCGCACGATGATATGGTCGATGATTTCTGCCAGCGGGGCGCTACGCCAGTCTTTCTCAATCGGTTGTTCAGCGAGCTTTGCCAGTTCAGCTTCAATGACCTCAACATCCAGTTCTTTACGTGCCGCCGCGCGCGCCAGCGTCTGCTTACCGCCACAGCAGTAATCC > NZ_CP009273/4421550‑4421720
|
tGGTAGCGCACGATGATATGGTCGATGATTTCTGCCAGCGGGGCGCTACGCCAGTCTTTCTCAATCGGTTGTTCAGCGAGCTTTGGCAGt > 1:452171/1‑90 (MQ=255)
ggTAGCGCACGATGATATGGTCGATGATTTCTGCCAGCGGGGCGCTACGCCAGTCTTTCTCAATCGGTTGTTCAGCGAGCTTTGGCAGtt < 2:873726/90‑1 (MQ=255)
aGCGCACGATGATATGGTCGATGATTTCTGCCAGCGGGGCGCTACGCCAGTCTTTCTCAATCGGTTGTTCAGCGAGCTTTGGCAGTTCAg < 1:481223/90‑1 (MQ=255)
gcgcACGATGATATGGTCGATGATTTCTGCCAGCGGGGCGCTACGCCAGTCTTTCTCAATCGGTTGTTCAGCGAGCTTTGGCAGTTCAGc > 2:57947/1‑90 (MQ=255)
atgatATGGTCGATGATTTCTGCCAGCGGGGCGCTACGCCAGTCTTTCTCAATCGGTTGTTCAGCGAGCTTTGGCAGTTCAGCTTCAATg > 2:356871/1‑90 (MQ=255)
tgatATGGTCGATGATTTCTGCCAGCGGGGCGCTACGCCAGTCTTTCTCAATCGGTTATTCAGCGAGCTTTGGCAGTTCAGCTTCAATGa < 1:462177/90‑1 (MQ=255)
gatATGGTCGATGATTTCTGCCAGCGGGGCGCTACGCCAGTCTTTCTCAATCGGTTGTTCAGCGAGCTTTGGCAGTTCAGCTTCAATGAc < 1:619522/90‑1 (MQ=255)
ggTCGATGATTTCTGCCAGCGGGGCGCTACGCCAGTCTTTCTCAATCGGTTGTTCAGCGAGCTTTGGCAGTTCAGCTTCAATGACCTCaa < 1:356871/90‑1 (MQ=255)
ggTCGATGATTTCTGCCAGCGGGGCGCTACGCCAGTCTTTCTCAATCGGTTGTTCAGCGAGCTTTGGCAGTTCAGCTTCAATGACCTCaa < 1:38074/90‑1 (MQ=255)
ggTCGATGATTTCTGCCAGCGGGGCGCTACGCCAGTCTTTCTCAATCGGTTGTTCAGCGAGCTTTGCCAGTTCAGCTTCAATGACCTCaa < 1:439910/90‑1 (MQ=255)
gTCGATGATTTCTGCCAGCGGGGCGCTACGCCAGTCTTTCTCAATCGGTTGTTCAGCGAGCTTTGGCAGTTCAGCTTCAATGACCTCAAc > 1:195419/1‑90 (MQ=255)
cGATGATTTCTGCCAGCGGGGCGCTACGCCAGTCTTTCTCAATCGGTTGTTCAGCGAGCTTTGGCAGTTCAGCTTCAATg > 2:427009/1‑80 (MQ=255)
cGATGATTTCTGCCAGCGGGGCGCTACGCCAGTCTTTCTCAATCGGTTGTTCAGCGAGCTTTGGCAGTTCAGCTTCAATg < 1:427009/80‑1 (MQ=255)
atgatTTCTGCCAGCGGGGCGCTACGCCAGTCTTTCTCAATCGGTTGTTCAGCGAGCTTTGGCAGTTCAGCTTCAATGACCTCAACATcc < 2:147718/90‑1 (MQ=255)
atgatTTCTGCCAGCGGGGCGCTACGCCAGTCTTTCTCAATCGGTTGTTCAGCGAGCTTTGGCAGTTCAGCTTCAATGACCTCAACATcc < 2:240008/90‑1 (MQ=255)
tgatTTCTGCCAGCGGGGCGCTACGCCAGTCTTTCTCAATCGGTTGTTCAGCGAGCTTTGGCAGTTCAGCTTCAATGACCTCAACATCCa < 2:452171/90‑1 (MQ=255)
tttCTGCCAGCGGGGCGCTACGCCAGTCTTTCTCAATCGGTTGTTCAGCGAGCTTTGGCAGTTCAGCTTCAATGACCTCAACATCCAGtt < 1:403857/90‑1 (MQ=255)
ttCTGCCAGCGGGGCGCTACGCCAGTCTTTCTCAATCGGTTGTTCAGCGAGCTTTGGCAGTTCAGCTTCAATGACCTCAACATCCAGTTc > 2:50623/1‑90 (MQ=255)
ttCTGCCAGCGGGGCGCTACGCCAGTCTTTCTCAATCGGTTGTTCAGCGAGCTTTGGCAGTTCAGCTTCAATGACCTCAACATCCAGTTc > 1:884685/1‑90 (MQ=255)
ggCGCTACGCCAGTCTTTCTCAATCGGTTGTTCAGCGAGCTTTGGCAGTTCAGCTTCAATGACCTCAACATCCAGTTCTTTACGTgccgc < 2:464216/90‑1 (MQ=255)
cgcTACGCCAGTCTTTCTCAATCGGTTGTTCAGCGAGCTTTGGCAGTTCAGCTTCAATGACCTCAACATCCAGTTCTTTACGTGccgccg < 1:728259/90‑1 (MQ=255)
cTACGCCAGTCTTTCTCAATCGGTTGTTCAGCGAGCTTTGGCAGTTCAGCTTCAATGACCTCAACATCCAGTTCTTTACGTGCCGCcgcg > 2:354279/1‑90 (MQ=255)
ccAGTCTTTCTCAATCGGTTGTTCAGCGAGCTTTGGCAGTTCAGCTTCAATGACCTCAACATCCAGTTCTTTACGTGCCGCCgcgcgcgc < 1:50623/90‑1 (MQ=255)
ccAGTCTTTCTCAATCGGTTGTTCAGCGAGCTTTGGCAGTTCAGCTTCAATGACCTAAACATCCAGTTCTTTACGTGCCGCCgcgcgcgc < 1:629507/90‑1 (MQ=255)
aGTCTTTCTCAATCGGTTGTTCAGCGAGCTTTGGCAGTTCAGCTTCAATGACCTCAACATCCAGTTCTTTACGTGCCGCCGCGCGCGCCa > 2:294302/1‑90 (MQ=255)
aTCGGTTGTTCAGCGAGCTTTGGCAGTTCAGCTTCAATGACCTCAACATCCAGTTCTTTACGTGCCGCCGCGCGCGCCAGCGTCTGCTTa > 2:173497/1‑90 (MQ=255)
cGGTTGTTCAGCGAGCTTTGGCAGTTCAGCTTCAATGCCCTCAACACCCAGTTCTTTACGTGCCGCCGCGCGCGCCAGCGTCTGCTTAcc < 2:160734/90‑1 (MQ=255)
ttgttCAGCGAGCTTTGGCAGTTCAGCTTCAATGCCCTCAACATCCAGTTCTTTACGTGCCGCCGCGCGCGCCAGCGTCTGCTTACCGcc < 2:42241/90‑1 (MQ=255)
ttgttCAGCGAGCTTTGGCAGTCCAGCTTCAATGCCCCCACCACCCAGTTCTTTACGTGCCCCCGCGCGCGCCAGCGTCTGCTTACCGcc < 2:474378/90‑1 (MQ=255)
ttgttCAGCGAGCTTCGCCAGTTCAGCTTCAATGACCTCAACATCCAGTTCTTTACGTGCCGCCGCGCGCGCCAGCGTCTGCTTACCGcc > 2:188201/1‑90 (MQ=255)
cAGCGAGCTTTGGCAGTTCAGCTTCAATGACCTCAACATCCATTTCTTTACGTGCCGCCGCGCGCGCCAGCGTCTGCTTACCGCCAcagc < 2:195419/90‑1 (MQ=255)
gCGAGCTTTGGCAGTTCAGCTTCAATGACCTCAACATCCAGTTCTTTACGTGCCGCCGCGCGCGCCAGCGTCTGCTTACCGCCAcagcag < 1:16090/90‑1 (MQ=255)
gCGAGCTTTGGCAGTTCAGCTTCAATGACCTCAACATCCAGTTCTTTACGTGCCGCCGCGCGCGCCAGCGTCTGCTTACCGCCAcagcag > 2:425373/1‑90 (MQ=255)
gCGAGCTTTGGCAGTTCAGCTTCAATGACCTCAACATCCAGTTC‑TTACGTGCCGCCGCGCGCGCCAGCGTCTGCTTACCGCCACAGCAGt > 2:772132/1‑90 (MQ=255)
gCGAGCTTTGGAAGTTCAGCTTCAATGCCCTCAACTTCCAGTTCTTTACGTGCCGCAGCGCGCGCCAGCGTCTGCTTACCGCCAcagcag < 1:330143/90‑1 (MQ=255)
cGAGCTTTGGCAGTTCAGCTTCAATGACCTCAACATCCAGTTCTTTACGTGCCGCCGCGCGCGCCAGCGTCTGCTTACCGCCACAGCAGt < 1:808839/90‑1 (MQ=255)
cGAGCTTTGGCAGTTCAGCTTCAATGACCTCAACACCCAGTTCTTTACGTGCCGCCGCGCGCGCCAGCGTCTGCTTACCGCCACAGCAGt < 2:705549/90‑1 (MQ=255)
gAGCTTTGGCAGTTCAGCTTAAATGCCCTCAACACCCAGTTCTTTACGTGCCGCCGCGCGCGCCAGCGTCTGCTTACCGCCACAGCAGTa < 2:425173/90‑1 (MQ=255)
aGCTTTGGCAGTTCAGCTTCAATGACCTCAACATCCAGTTCTTTACGTGCCGCCGCGCGCGCCAGCGTCTGCTTACCGCCACAGCAGTaa < 1:564612/90‑1 (MQ=255)
cTTTGGCAGTTCGGCTTCAATGACCTCAACATCCAGTTC‑TTACGTGCCGCCGCGCGCGCCAGCGTCTGCTTACCGCCACAGCAGTAATcc < 1:772132/90‑1 (MQ=255)
cTTTGGCAGTTCAGCTTCAATGACCTCAACATCCAGTTCTTTACGTGCCGCCGCGCGCGCCAGCGTCTGCTTACCGCCACAGCAGTAATc < 1:201820/90‑1 (MQ=255)
cTTTGGCAGTTCAGCTTCAATGACCTCAACATCCAGTTCTTTACGTGCCGCCGCGCGCGCCAGCGTCTGCTTACCGCCACAGCAGTAATc < 1:294302/90‑1 (MQ=255)
cTTTGCCAGTTCAGCTCCACTGCCCTCACCACCCAGTTTTTTCCGTCCCGCCGCCCGCGCCAGCGTCTGCTTACCGCCACAGCAGTAATc < 2:626772/90‑1 (MQ=255)
|
TGGTAGCGCACGATGATATGGTCGATGATTTCTGCCAGCGGGGCGCTACGCCAGTCTTTCTCAATCGGTTGTTCAGCGAGCTTTGCCAGTTCAGCTTCAATGACCTCAACATCCAGTTCTTTACGTGCCGCCGCGCGCGCCAGCGTCTGCTTACCGCCACAGCAGTAATCC > NZ_CP009273/4421550‑4421720
|
| Alignment Legend |
|---|
Aligned base mismatch/match (shaded by quality score): ATCG/ATCG < 3 ≤ ATCG/ATCG < 8 ≤ ATCG/ATCG < 23 ≤ ATCG/ATCG < 33 ≤ ATCG/ATCG < 41 ≤ ATCG/ATCG |
Unaligned base: atcg Masked matching base: atcg Alignment gap: ‑ Deleted base: ‑ |
GATK/CNVnator alignment
BRESEQ :: bam2aln output
GTGACGATCGTGGTAGCGCACGATGATATGGTCGATGATTTCTGCCAGCGGGGCGCTACGCCAGTCTTTCTCAATCGGTTGTTCAGCGAGCTTTGCCAGTTCAGCTTCAATGACCTCAACATCCAGTTCTTTACGTGCCGCCGCGCGCGCCAGCGTCTGCTTACCGCCACAGCAGTAATCCATATCATATT > NZ_CP009273/4421540‑4421730
|
GTGACGATCGTGGTAGCGCACGATGATATGGTCGATGATTTCTGCCAGCGGGGCGCTACGCCAGTCTTTCTCAATCGGTTGTTCAGCGAGCTTTGGCAGT > SRR3722072.460446/1‑100 (MQ=60)
GATCGTGGTAGCGCACGATGATATGGTCGATGATTTCTGCCAGCGGGGCGCTACGCCAGTCTTTCTCAATCGGTTGTTCAGCGAGCTTTGGCAGTTCAGC < SRR3722072.354725/100‑1 (MQ=60)
TCGTGGTAGCGCACGATGATATGGTCGATGATTTCTGCCAGCGGGGCGCTACGCCAGTCTTTCTCAATCGGTTGTTCAGCGAGCTTTGGCAGTTCAGCTT < SRR3722072.381443/100‑1 (MQ=60)
AGCGCACGATGATATGGTCGATGATTTCTGCCAGCGGGGCGCTACGCCAGTCTTTCTCAATCGGTTGTTCAGCGAGCTTTGGCAGTTCAGCTTCAATGAC < SRR3722072.489950/100‑1 (MQ=60)
CGATGATATGGTCGATGATTTCTGCCAGCGGGGCGCTACGCCAGTCTTTCTCAATCGGTTGTTCAGCGAGCTTTGGCAGTTCAGCTTCAATGACCTCAAC > SRR3722072.198797/1‑100 (MQ=60)
ATGATATGGTCGATGATTTCTGCCAGCGGGGCGCTACGCCAGTCTTTCTCAATCGGTTGTTCAGCGAGCTTTGGCAGTTCAGCTTCAATGACCTCAACAT < SRR3722072.434779/100‑1 (MQ=60)
TGATATGGTCGATGATTTCTGCCAGCGGGGCGCTACGCCAGTCTTTCTCAATCGGTTATTCAGCGAGCTTTGGCAGTTCAGCTTCAATGACCTCAACATC < SRR3722072.470639/100‑1 (MQ=60)
GATATGGTCGATGATTTCTGCCAGCGGGGCGCTACGCCAGTCTTTCTCAATCGGTTGTTCAGCGAGCTTTGGCAGTTCAGCTTCAATGACCTCAACATCC < SRR3722072.630576/100‑1 (MQ=60)
GGTCGATGATTTCTGCCAGCGGGGCGCTACGCCAGTCTTTCTCAATCGGTTGTTCAGCGAGCTTTGGCAGTTCAGCTTCAATGACCTCAACATCCAGTTC > SRR3722072.899912/1‑100 (MQ=60)
GGTCGATGATTTCTGCCAGCGGGGCGCTACGCCAGTCTTTCTCAATCGGTTGTTCAGCGAGCTTTGGCAGTTCAGCTTCAATGACCTCAACATCCAGTTC < SRR3722072.38755/100‑1 (MQ=60)
GGTCGATGATTTCTGCCAGCGGGGCGCTACGCCAGTCTTTCTCAATCGGTTGTTCAGCGAGCTTTGGCAGTTCAGCTTCAATGACCTCAACACCCAGTTC < SRR3722072.363184/100‑1 (MQ=60)
GGTCGATGATTTCTGCCAGCGGGGCGCTACGCCAGTCTTTCTCAATCGGTTGTTCAGCGAGCTTTGCCAGTTCAGCTTCAATGACCTCAACATCCAGTTC < SRR3722072.447948/100‑1 (MQ=60)
TTTCTGCCAGCGGGGCGCTACGCCAGTCTTTCTCAATCGGTTGTTCAGCGAGCTTTGGCAGTTCAGCTTCAATGACCTCAACATCCAGTTCTTTACGTGC < SRR3722072.411141/100‑1 (MQ=60)
CGCTACGCCAGTCTTTCTCAATCGGTTGTTCAGCGAGCTTTGGCAGTTCAGCTTCAATGACCTCAACATCCAGTTCTTTACGTGCCGCCGCGCGCGCCAG < SRR3722072.741182/100‑1 (MQ=60)
CCAGTCTTTCTCAATCGGTTGTTCAGCGAGCTTTGGCAGTTCAGCTTCAATGACCTCAACATCCAGTTCTTTACGTGCCGCCGCGCGCGCCAGCGTCTGC < SRR3722072.51548/100‑1 (MQ=60)
CCAGTCTTTCTCAATCGGTTGTTCAGCGAGCTTTGGCAGTTCAGCTTCAATGACCTAAACATCCAGTTCTTTACGTGCCGCCGCGCGCGCCAGCGTCTGC < SRR3722072.640746/100‑1 (MQ=60)
GCGAGCTTTGGCAGTTCAGCTTCAATGACCTCAACATCCAGTTCTTTACGTGCCGCCGCGCGCGCCAGCGTCTGCTTACCGCCACAGCAGTAATCCATAT < SRR3722072.16393/100‑1 (MQ=60)
GCGAGCTTTGGAAGTTCAGCTTCAATGCCCTCAACTTCCAGTTCTTTACGTGCCGCAGCGCGCGCCAGCGTCTGCTTACCGCCACAGCAGTAATCCATAT < SRR3722072.335940/100‑1 (MQ=60)
CGAGCTTTGGCAGTTCAGCTTCAATGACCTCAACATCCAGTTCTTTACGTGCCGCCGCGCGCGCCAGCGTCTGCTTACCGCCACAGCAGTAATCCATATC < SRR3722072.822941/100‑1 (MQ=60)
AGCTTTGGCAGTTCAGCTTCAATGACCTCAACATCCAGTTCTTTACGTGCCGCCGCGCGCGCCAGCGTCTGCTTACCGCCACAGCAGTAATCCATATCAT < SRR3722072.574730/100‑1 (MQ=60)
GCTTTGGCAGTTCAGCTTCAATGACCTCAACATCCAGTTCTTTACGTGCCGCCGCGCGCGCCAGCGTCTGCTTACCGCCACAGCAGTAATCCATATCATA > SRR3722072.153081/1‑100 (MQ=60)
CTTTGGCAGTTCGGCTTCAATGCCCTCAACATCCAGTTC‑TTACGTGCCGCCGCGCGCGCCAGCGTCTGCTTACCGCCACAGCAGTAATCCATATCATATT < SRR3722072.785699/100‑1 (MQ=60)
CTTTGGCAGTTCAGCTTCAATGACCTCAACATCCAGTTCTTTACGTGCCGCCGCGCGCGCCAGCGTCTGCTTACCGCCACAGCAGTAATCCATATCATAT < SRR3722072.299396/100‑1 (MQ=60)
CTTTGGCAGTTCAGCTTCAATGACCTCAACATCCAGTTCTTTACGTGCCGCCGCGCGCGCCAGCGTCTGCTTACCGCCACAGCAGTAATCCATATCATAT < SRR3722072.205298/100‑1 (MQ=60)
|
GTGACGATCGTGGTAGCGCACGATGATATGGTCGATGATTTCTGCCAGCGGGGCGCTACGCCAGTCTTTCTCAATCGGTTGTTCAGCGAGCTTTGCCAGTTCAGCTTCAATGACCTCAACATCCAGTTCTTTACGTGCCGCCGCGCGCGCCAGCGTCTGCTTACCGCCACAGCAGTAATCCATATCATATT > NZ_CP009273/4421540‑4421730
|
| Alignment Legend |
|---|
Aligned base mismatch/match (shaded by quality score): ATCG/ATCG < 0 ≤ ATCG/ATCG < 19 ≤ ATCG/ATCG < 29 ≤ ATCG/ATCG < 34 ≤ ATCG/ATCG < 41 ≤ ATCG/ATCG |
Unaligned base: atcg Masked matching base: atcg Alignment gap: ‑ Deleted base: ‑ |
