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 F21 I0 R1
|
476 |
35.3 |
2812105 |
96.7% |
2719305 |
61.2 |
Breseq alignment
BRESEQ :: Evidence
|
| evidence |
seq id |
position |
mutation |
freq |
annotation |
gene |
description |
| RA |
W3110S.gb |
3,211,677 |
C→T |
9.4% |
intergenic (+169/‑26) |
dnaG → / → rpoD |
DNA primase/RNA polymerase, sigma 70 (sigma D) factor |
|
| |
seq id |
position |
ref |
new |
freq |
score (cons/poly) |
reads |
annotation |
genes |
product |
| * | W3110S.gb | 3,211,677 | 0 | C | T | 9.4%
| 159.3
/ 6.2
| 53 | intergenic (+169/‑26) | dnaG/rpoD | DNA primase/RNA polymerase, sigma 70 (sigma D) factor |
| Reads supporting (aligned to +/- strand): ref base C (24/24); new base T (3/2); total (27/26) |
| Fisher's exact test for biased strand distribution p-value = 1.00e+00 |
| Kolmogorov-Smirnov test that lower quality scores support variant p-value = 8.68e-01 |
AAACAACCGTTGGATTTCAGCGTTAACGGCTGAAGGACATCGGGTCAATCGCCCAACACCAACCTCATGAAATAAGTGTGGATACCGTCTTATGGAGCAAAACCCGCAGTCACAGCTGAAACTTCTTGTCACC > W3110S.gb/3211612‑3211744
|
aaaCAACCGTTGGATTTCAGCGTTAACGGCTGAAGGACATCGGGTCAATCGCCCAACACCAACCTCATGa > 1:1508158/1‑70 (MQ=255)
aacaacCGTTGGATTTCAGCGTTAACGGCTGAAGGACATCGGGTCAATCGCCCAACACCAACCTCATGaaa > 1:1708140/1‑71 (MQ=255)
aacaacCGTTGGATTTCAGCGTTAACGGCTGAAGGACATCGGGTCAATCGCCCAACACCAACCTCATGaaa > 1:1620267/1‑71 (MQ=255)
acaacCGTTGGATTTCAGCGTTAACGGCTGAAGGACATCGGGTCAATCGCCCAACACCAACCTCATGAAAt < 1:54494/71‑1 (MQ=255)
caacCGTTGGATTTCAGCGTTAACGGCTGAAGGACATCGGGTCAATCGCCCAACACCAACCTCATGAAAt > 1:504053/1‑70 (MQ=255)
ttGGATTTCAGCGTTAACGGCTGAAGGACATCGGGTCAATCGCCCAACACCAACCTCATGAAATAAGtgtg > 1:1244920/1‑71 (MQ=255)
ttGGATTTCAGCGTTAACGGCTGAAGGACATCGGGTCAATCGCCCAACACCAACCTCATGAAATAAGtgtg < 1:345362/71‑1 (MQ=255)
tGGATTTCAGCGTTAACGGCTGAAGGACATCGGGTCAATCGCCCAACACCAACCTCATGAAATAAgtg > 1:1152296/1‑68 (MQ=255)
tCAGCGTTAACGGCTGAAGGACATCGGGTCAATCGCCCAACACCAACCTCATGAAATAAGTGTGGATACCg > 1:2213439/1‑71 (MQ=255)
gCGTTAACGGCTGAAGGACATCGGGTCAATCGCCCAACACCAACCTCATGAAATAAGTGTGGATACCGTCt < 1:249239/71‑1 (MQ=255)
gTTAACGGCTGAAGGACATCGGGTCAATCGCCCAACACCAACCTTATGAAATAAGTGTGGATACCGTCTTa < 1:569545/71‑1 (MQ=255)
gTTAACGGCTGAAGGACATCGGGTCAATCGCCCAACACCAACCTTATGAAATAAGTGTGGATACCGTCTTa < 1:566236/71‑1 (MQ=255)
tAACGGCTGAAGGACATCGGGTCAATCGCCCAACACCAACCTCATGAAATAAGtgtg < 1:1808299/57‑1 (MQ=255)
tAACGGCTGAAGGACATCGGGTCAATCGCCCAACACCAACCTCATGAAATAAGtgtg < 1:1736702/57‑1 (MQ=255)
aaCGGCTGAAGGACATCGGGTCAATCGCCCAACACCAACCTCATGAAATAAGTGTGGATACCGt > 1:546882/1‑64 (MQ=255)
aaCGGCTGAAGGACATCGGGTCAATCGCCCAACACCAACCTCATGAAATAAGTGTGGATACCGTCTTATg < 1:920025/70‑1 (MQ=255)
cGGCTGAAGGACATCGGGTCAATCGCCCAACACCAACCTCATGAAATAAGTGTGGATACCGTCt < 1:2408426/64‑1 (MQ=255)
gCTGAAGGACATCGGGTCAATCGCCCAACACCAACCTCATGAAATAAGTGTGGATACAGTCTTa > 1:1346145/1‑64 (MQ=255)
cTGAAGGACATCGGGTCAATCGCCCAACACCAACCTCATGAAATAAGTGTGGATACCGTCTTATGGAGCaa < 1:1994484/71‑1 (MQ=255)
tGAAGGACATCGGGTCAATCGCCCAACACCAACCTCATGAAATAAGTGTGGa > 1:569832/1‑52 (MQ=255)
tGAAGGACATCGGGTCAATCGCCCAACACCAACCTCATGAAATAAGTGTGGATACCGTCTTATGGAGCaa > 1:1759009/1‑70 (MQ=255)
aaGGACATCGGGTCAATCGCCCAACACCAACCTCATGAAATTAGTGTGGAt < 1:1758941/51‑1 (MQ=255)
aaGGACATCGGGTCAATCGCCCAACACCAACCTCATGAAATAAGtgtg < 1:2593301/48‑1 (MQ=255)
aaGGACATCGGGTCAATCGCCCAACACCAACCTCATGAAATAAGTGTGGAt < 1:95323/51‑1 (MQ=255)
aGGACATCGGGTCAATCGCCCAACACCAACCTCATGAAATAAg < 1:1322655/43‑1 (MQ=255)
aGGACATCGGGTCAATCGCCCAACACCAACCTCATGAAATAAg < 1:2690238/43‑1 (MQ=255)
cATCGGGTCAATCGCCCAACACCAACCTCATGAAATAAGtgtg < 1:535495/43‑1 (MQ=255)
cATCGGGTCAATCGCCCAACACCAACCTCATGAAATAAGtgtg < 1:2006926/43‑1 (MQ=255)
cGGGTCAATCGCCCAACACCAACCTCATGAAATAAGTGTGGa > 1:1627340/1‑42 (MQ=255)
gggTCAATCGCCCAACACCAACCTTATGAAATAAGTGTGGATACCGTCTTATg > 1:2123081/1‑53 (MQ=255)
gggTCAATCGCCCAACACCAACCTTATGAAATAAGTGTGGATACCGTCTTATGGAGCAAAACCCGCAGTca > 1:144186/1‑71 (MQ=255)
gTCAATCGCCCAACACCAACCTCATGAAATAAGtgtg < 1:480048/37‑1 (MQ=255)
gTCAATCGCCCAACACCAACCTCATGAAATAAGtgtg < 1:456202/37‑1 (MQ=255)
tCAATCGCCCAACACCAACCTTATGAAATAAGTGTGGATACCGTCTTATGGAg > 1:1664730/1‑53 (MQ=255)
tCGCCCAACACCAACCTCATGAAATAAGTGTGGATACCGTCt < 1:563720/42‑1 (MQ=255)
tCGCCCAACACCAACCTCATGAAATAAGTGTGGATACCGTCTTATGGAGCaaaa < 1:1168255/54‑1 (MQ=255)
tCGCCCAACACCAACCTCATGAAATAAGTGTGGATACCGTCTTATGGAGCAAAACCCGCAGTCACAGCTGa < 1:391166/71‑1 (MQ=255)
tccccATCACCAACCTCATGAAATAAGTGTGGATACCGTCTTATGGAGCAAAACCCGCAGTCACAGCTGaa < 1:2524589/69‑1 (MQ=255)
cGCCCAACACCAACCTCATGAAATAAGTGTGGATACCGTCTTATGGAGCAAAAc > 1:803961/1‑54 (MQ=255)
cGCCCAACACCAACCTCATGAAATAAGTGTGGATACCGTCTTATGGAGCAAAAc > 1:1602934/1‑54 (MQ=255)
cGCCCAACACCAACCTCATGAAATAAGTGTGGATACCGTCTTATGGAGCAAAAc > 1:1185695/1‑54 (MQ=255)
gCCCAACACCAACCTCATGAAATAAGTGTGGATACCGTCTTa > 1:1909482/1‑42 (MQ=255)
gCCCAACACCAACCTCATGAAATAAGTGTGGATACCGTCTTATGGAGCAAAACCCGCAGTCACAGCTGaaa > 1:761870/1‑71 (MQ=255)
gCCCAACACCAACCTCATGAAATAAGTGTGGATACCGTCTTATGGAGCAAAACCCGCAGTCACAGCTGaaa > 1:2691437/1‑71 (MQ=255)
gCCCAACACCAACCTCATGAAATAAGTGTGGATACCGTCTTATGGAGCAAAACCCGCAGTCACAGCTGaaa > 1:1465960/1‑71 (MQ=255)
acacCAACCTCATGAAATAAGTGTGGATACCGTCTTATGGAGCAAAACCCGCAGTCACAGCTGAAActtct > 1:1931270/1‑71 (MQ=255)
acacCAACCTCATGAAATAAGTGTGGATACCGTCTTATGGAGCAAAACCCGCAGTCACAGCTGAAActtct > 1:1255740/1‑71 (MQ=255)
cacCAACCTCATGAAATAAGTGTGGATACCGTCTTATGGAGCAAAACCCGCAGTCACAGCTGAAActtctt < 1:2044136/71‑1 (MQ=255)
acCAACCTCATGAAATAAGTGTGGATACCGTCTTATGGAGCAAAACCCGCAGTCACAGCTGAAACTTCTTg > 1:2543293/1‑71 (MQ=255)
ccAACCTCATGAAATAAGTGTGGATACCGTCTTATGGAGCAAAACCCGCAGTca > 1:1076772/1‑54 (MQ=255)
aaCCTCATGAAATAAGTGTGGATACCGTCTTATGGAGCAAAACCCGCAGTCACAGCTGAAACTTCTTg > 1:306433/1‑68 (MQ=255)
ccTCATGAAATAAGTGTGGATACCGTCTTATGGAGCAAAACCCGCAGTCACAGCTGAAACTTCTTGTCAcc < 1:1602029/71‑1 (MQ=255)
cTCATGAAATAAGTGTGGATACCGTCTTATGGAGCAAAACCCGCAGTCACAGCTGa < 1:1022918/56‑1 (MQ=255)
cATGAAATAAGTGTGGATACCGTCTTATGGAGCAAAACCCGCAGTCACAGCTGaaa > 1:2152846/1‑56 (MQ=255)
cATGAAATAAGTGTGGATACCGTCTTATGGAGCAAAACCCGCAGTCACAGCTGaaa > 1:1862912/1‑56 (MQ=255)
|
AAACAACCGTTGGATTTCAGCGTTAACGGCTGAAGGACATCGGGTCAATCGCCCAACACCAACCTCATGAAATAAGTGTGGATACCGTCTTATGGAGCAAAACCCGCAGTCACAGCTGAAACTTCTTGTCACC > W3110S.gb/3211612‑3211744
|
| 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
