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 F3 I0 R1
|
560 |
56.4 |
4650532 |
94.9% |
4413354 |
59.3 |
Breseq alignment
BRESEQ :: Evidence
|
| evidence |
seq id |
position |
mutation |
freq |
annotation |
gene |
description |
| RA |
W3110S.gb |
4,295,216 |
G→A |
35.5% |
G38D (GGC→GAC) |
nrfE → |
heme lyase (NrfEFG) for insertion of heme into c552, subunit NrfE |
|
| |
seq id |
position |
ref |
new |
freq |
score (cons/poly) |
reads |
annotation |
genes |
product |
| * | W3110S.gb | 4,295,216 | 0 | G | A | 35.5%
| 64.7
/ 56.6
| 62 | G38D (GGC→GAC) | nrfE | heme lyase (NrfEFG) for insertion of heme into c552, subunit NrfE |
| Reads supporting (aligned to +/- strand): ref base G (21/19); new base A (12/10); total (33/29) |
| Fisher's exact test for biased strand distribution p-value = 1.00e+00 |
| Kolmogorov-Smirnov test that lower quality scores support variant p-value = 8.00e-01 |
CCTGCCATGATGCGACTCACTTGCATCGGCATTCTGGCGCAGTTCGCGCTCCTGCTGCTCGCCTTTGGCGTACTGACGTATTGTTTTCTCATCAGCGATTTCTCGGTCATTTATGTCGCGCAACATAGCTATAGCCT > W3110S.gb/4295149‑4295285
|
ccTGCCATGATGCGACTCACTTGCATCGGCATTCTGGCGCAGTTCGCGCTCCTGCTGCTCGCCTTTGGCGt < 1:4008090/71‑1 (MQ=255)
cATGATGCGACTCACTTGCATCGGCATTCTGGCGCAGTTCGCGCTCCTGCTGCTCGCCTTTGACGTACTGa > 1:996914/1‑71 (MQ=255)
tgatgCGACTCACTTGCATCGGCATTCTGGCGCAGTTCGCGCTCCTGCTGCTCGCCTTTGGCGTACTGAc < 1:584747/70‑1 (MQ=255)
cTCACTTGCATCGGCATTCTGGCGCAGTTCGCGCTCCTGCTGCTCGCCTTTGGCGTACTGACGTATTGttt < 1:1599531/71‑1 (MQ=255)
aCTTGCATCGGCATTCTGGCGCAGTTCGCGCTCCTGCTGCTCGCCTTTGACGt > 1:3999287/1‑53 (MQ=255)
cTTGCATCGGCATTCTGGCGCAGTTCGCGCTCCTGCTGCTCGCCTTTGACGTACTGACGTATTGTTTtctc < 1:2167636/71‑1 (MQ=255)
ttGCATCGGCATTCTGGCGCAGTTCGCGCTCCTGCTGCTCGCCTTTGGCGTACTGACGTa < 1:2204438/60‑1 (MQ=255)
tGCATCGGCATTCTGGCGCAGTTCGCGCTCCTGCTGCTCGCCTTTGACGTACTGACGTATTGTTTTCtcat > 1:1817796/1‑71 (MQ=255)
tGCATCGGCATTCTGGCGCAGTTCGCGCTCCTGCTGCTCGCCTTTGACGTACTGACGTATTGTTTTCtca > 1:3231908/1‑70 (MQ=255)
gCATCGGCATTCTGGCGCAGTTCGCGCTCCTGCTGCTCGCCTTTGGCGTACTGACGTATTGtttt > 1:2975272/1‑65 (MQ=255)
cATCGGCATTCTGGCGCAGTTCGCGCTCCTGCTGCTCGCCTTTGGCGTACTGACGTATTGTTTTCtcatc < 1:1163640/70‑1 (MQ=255)
ggCATTCTGGCGCAGTTCGCGCTCCTGCTGCTCGCCTTTGGCGt > 1:2387523/1‑44 (MQ=255)
ggCATTCTGGCGCAGTTCGCGCTCCTGCTGCTCGCCTTTGACGTACTGACGTATTGTTTTCTCATCAGCg < 1:1938152/70‑1 (MQ=255)
ggCATTCTGGCGCAGTTCGCGCTCCTGCTGCTCGCCTTTGACGTACTGACGTATTGTTTTCTCATCAGCGa > 1:3820385/1‑71 (MQ=255)
gCATTCTGGCGCAGTTCGCGCTCCTGCTGCTCGCCTTTGGCGTACt > 1:4493186/1‑46 (MQ=255)
gCATTCTGGCGCAGTTCGCGCTCCTGCTGCTCGCCTTTGGCGTACTGACGTa < 1:1691628/52‑1 (MQ=255)
gCATTCTGGCGCAGTTCGCGCTCCTGCTGCTCGCCTTTGGCGTACTGACGTATTg < 1:3805371/55‑1 (MQ=255)
cATTCTGGCGCAGTTCGCGCTCCTGCTGCTCGCCTTTGGCGTACTGACGTATTGTTTTATCATCAGCGAtt > 1:2037314/1‑71 (MQ=255)
ttCTGGCGCAGTTCGCGCTCCTGCTGCTCGCCTTTGACGTACTGACGTATTGTTTTCTCATCAGCGATTtc < 1:3241073/71‑1 (MQ=255)
ttCTGGCGCAGTTCGCGCTCCTGCTGCTCGCCTTTGACGTACTGACGTATTGTTTTCTCATCAGCGATTtc < 1:2390465/71‑1 (MQ=255)
cTGGCGCAGTTCGCGCTCCTGCTGCTCGCCTTTGGCGTACTGACGTATTGTTTtct < 1:1875010/56‑1 (MQ=255)
cgcAGTTCGCGCTCCTGCTGCTCGCCTTTGGCGTACTGACGTATTGTTTTCTCATCAGCGATTTCTCGGt > 1:2631863/1‑70 (MQ=255)
gcAGTTCGCGCTCCTGCTGCTCGCCTTTGGCGTACTGACGTATTGTTTTCtcatc > 1:2455543/1‑55 (MQ=255)
gcAGTTCGCGCTCCTGCTGCTCGCCTTTGACGTACTGACGTATTGTTTTCTCATCAGCGATTTCTCGGTCa < 1:2083953/71‑1 (MQ=255)
gcAGTTCGCGCTCCTGCTGCTCGCCTTTGACGTACTGACGTATTGTTTTCTCATCAGCGATTTCTCGGTCa < 1:634780/71‑1 (MQ=255)
gTTCGCGCTCCTGCTGCTCGCCTTTGGCGTACTGACGTATTGTTTTCTCATCAGCGATTTCTCGGTCAttt < 1:2579767/71‑1 (MQ=255)
ttCGCGCTCCTGCTGCTCGCCTTTGGCGTACTGACGTAtt < 1:3771367/40‑1 (MQ=255)
ttCGCGCTCCTGCTGCTCGCCTTTGGCGTACTGACGTATTg < 1:2377576/41‑1 (MQ=255)
ttCGCGCTCCTGCTGCTCGCCTTTGGCGTACTGACGTATTGtt < 1:2784672/43‑1 (MQ=255)
ttCGCGCTCCTGCTGCTCGCCTTTGGCGTACTGACGTATTGtt < 1:4475214/43‑1 (MQ=255)
ttCGCGCTCCTGCTGCTCGCCTTTGGCGTACTGACGTATTGTTTTCTCATCAGCGATTTCTCGGTCa < 1:2191574/67‑1 (MQ=255)
ttCGCGCTCCTGCTGCTCGCCTTTGACGTACTGACGTATTGTTTTCTCATCAGCGAt < 1:2555904/57‑1 (MQ=255)
ttCGCGCTCCTGCTGCTCGCCTTTGACGTACTGACGTATTGTTTTCTCATCAGCGAt < 1:4617706/57‑1 (MQ=255)
tCGCGCTCCTGCTGCTCGCCTTTGGCGTACTGACGTATTGTTTTCtcatca > 1:1020409/1‑51 (MQ=255)
tCGCGCTCCTGCTGCTCGCCTTTGGCGTACTGACGTATTGTTTTCtcatca > 1:601468/1‑51 (MQ=255)
tCGCGCTCCTGCTGCTCGCCTTTGGCGTACTGACGTATTGTTTTCtcat > 1:2543804/1‑49 (MQ=255)
cgcgCTCCTGCTGCTCGCCTTTGGCGTACTGACGTATTGTTTTCtca > 1:1231626/1‑47 (MQ=255)
cgcgCTCCTGCTGCTCGCCTTTGGCGTACTGACGTATTGTTTTCTCATCAGCGATTTCTCGGTCATTTATg > 1:4128921/1‑71 (MQ=255)
cgcgCTCCTGCTGCTCGCCTTTGACGTACTGACGTATTGTTTTCTCATCAGCGa > 1:842795/1‑54 (MQ=255)
cgcgCTCCTGCTGCTCGCCTTTGACGTACTGACGTATTGTTTTCTCATCAGCGATTTCTCGGTCATTTa > 1:1391583/1‑69 (MQ=255)
cgcgCTCCTGCTGCTCGCCTTTGACGTACTGACGTATTGTTTTCTCATCAGCGATTTCTCGGTCATTTAt < 1:1121137/70‑1 (MQ=255)
cgcgCTCCTGCTGCTCGCCTTTGACGTACTGACGTATTGTTTTCTCATCAGCGATTTCTCGGTCATTTATg > 1:299875/1‑71 (MQ=255)
cgcgCTCCTGCTGCTCGCCTTTGACGTACTGACGTATTGGTTTCTCATCAGCGATTTCTCGGTCATTTATg > 1:4346455/1‑71 (MQ=255)
gcgcTCCTGCTGCTCGCCTTTGACGTACTGACGTATTGTTTTCTCATCAGCGATTTCTCGGTCATTTATGt < 1:1135129/71‑1 (MQ=255)
cgcTCCTGCTGCTCGCCTTTGGCGTACTGACGTATTGTTTTCTCATCAGCGATTTCTCGGTCATTTATGTc < 1:4409384/71‑1 (MQ=255)
ccTGCTGCTCGCCTTTGGCGTACTGACGTATTGTTTTCTCATCAGCGATTTCTCGGTCATTTATGTcgcg > 1:3499024/1‑70 (MQ=255)
ccTGCTGCTCGCCTTTGGCGTACTGACGTATTGTTTTCTCATCAGCGATTTCTCGGTCATTTATGTcgcg > 1:74305/1‑70 (MQ=255)
ccTGCTGCTCGCCTTTGACGTACTGACGTATTGTTTTCTCATCAGCGATTTCTCGGTCATTTATGTcgcg > 1:136207/1‑70 (MQ=255)
ctgctgCTCGCCTTTGACGTACTGACGTATTGTTTTCTCATCAGCGATTTCTCGGTCATTTATGTCgcgc > 1:2810681/1‑70 (MQ=255)
tgctgcTCGCCTTTGGCGTACTGACGTATTGTTTTCTCATCAGCGATTTCTCGGTCATTTATGTCGCGCaa > 1:3202624/1‑71 (MQ=255)
gctgctCGCCTTTGGCGTACTGACGTATTGTTTTCTCATCAGCGATTTCTCGGt > 1:3208017/1‑54 (MQ=255)
ctgctCGCCTTTGGCGTACTGACGTATTGTTTTCTCATCAGCGATTTCTCGGTCATTTATGTCGCGCaa < 1:366542/69‑1 (MQ=255)
ctgctCGCCTTTGGCGTACTGACGTATTGTTTTCTCATCAGCGATTTCTCGGTCATTTATGTCGCGCaa < 1:3708166/69‑1 (MQ=255)
tgctCGCCTTTGGCGTACTGACGTATTGTTTTCTCATCAGCGATTTCTCGGTCATTTATGTCGCGCAAc > 1:1226612/1‑69 (MQ=255)
gctCGCCTTTGGCGTACTGACGTATTGTTTTCTCATCAGCGATTTCTCGGTCATTTATGTCGCGCAACa > 1:1586759/1‑69 (MQ=255)
ctCGCCTTTGGCGTACTGACGTATTGTTTTCTCATCAGCGATTTCTCGGTCATTTa > 1:1272563/1‑56 (MQ=255)
ctCGCCTTTGACGTATTGACGTATTGTTTTCTCATCAGCGATTTCTCGGTCATTTATGTCGCGCAACa > 1:1209312/1‑68 (MQ=255)
tCGCCTTTGGCGTACTGACGTATTGTTTTCTCATCAGCGATTTCTCGGTCATTTATGTCGCGCaa < 1:456497/65‑1 (MQ=255)
gCCTTTGGCGTACTGACGTATTGTTTTCTCATCAGCGATTTCTCGGTCATTTATGTCGAGCAACGTa > 1:4218446/1‑67 (MQ=255)
tttGGCGTACTGACGTATTGTTTTCTCATCAGCGATTTCTCGGTCATTTATGTCGCGCa < 1:1859179/59‑1 (MQ=255)
tGGCGTACTGACGTATTGTTTTCTCATCAGCGAttt > 1:3037082/1‑36 (MQ=255)
tGGCGTACTGACGTATTGTTTTCTCATCAGCGATTTCTCGGTCATTTa > 1:1013064/1‑48 (MQ=255)
ggCGTACTGACGTATTGTTTTCTCATCAGCGATTTCTCGGTCATTTATGTCGCGCAACATAGCTATAGCct > 1:1122604/1‑71 (MQ=255)
|
CCTGCCATGATGCGACTCACTTGCATCGGCATTCTGGCGCAGTTCGCGCTCCTGCTGCTCGCCTTTGGCGTACTGACGTATTGTTTTCTCATCAGCGATTTCTCGGTCATTTATGTCGCGCAACATAGCTATAGCCT > W3110S.gb/4295149‑4295285
|
| Alignment Legend |
|---|
Aligned base mismatch/match (shaded by quality score): ATCG/ATCG < 3 ≤ ATCG/ATCG < 14 ≤ ATCG/ATCG < 32 ≤ ATCG/ATCG < 36 ≤ ATCG/ATCG |
Unaligned base: atcg Masked matching base: atcg Alignment gap: ‑ Deleted base: ‑ |
GATK/CNVnator alignment
N/A
