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 |
2,469,991 |
T→C |
32.8% |
S155G (AGC→GGC) |
vacJ ← |
predicted lipoprotein |
|
| |
seq id |
position |
ref |
new |
freq |
score (cons/poly) |
reads |
annotation |
genes |
product |
| * | W3110S.gb | 2,469,991 | 0 | T | C | 32.8%
| 68.2
/ 55.7
| 61 | S155G (AGC→GGC) | vacJ | predicted lipoprotein |
| Reads supporting (aligned to +/- strand): ref base T (20/21); new base C (10/10); total (30/31) |
| Fisher's exact test for biased strand distribution p-value = 1.00e+00 |
| Kolmogorov-Smirnov test that lower quality scores support variant p-value = 6.70e-01 |
CAGGAAAGAACCGGGTAAAAACCATCCGCCATATCACCACCGTCATCACGCAGCGTGAAGCTACCGTAGAACGGTAACTGAACGTAAGGCCCATAACCCACGCCATAATGACCAAGCGTACTACCGA > W3110S.gb/2469930‑2470056
|
cAGGAAAGAACCGGGTAAAAACCATCCGCCATATCACCACCGTCATCACGCAGCGTGAAGCTACCGTAGa < 1:765046/70‑1 (MQ=255)
aGGAAAGAACCGGGTAAAAACCATCCGCCATATCACCACCGTCATCACGCAGCGTGAAGCTACCGTAGAAc > 1:751205/1‑71 (MQ=255)
aaaGAACCGGGTAAAAACCATCCGCCATATCACCACCGTCATCACGCAGCGTGAAGCTACCg > 1:1046935/1‑62 (MQ=255)
aaGAACCGGGTAAAAACCATCCGCCATATCACCACCGTCATCACGCAGCGTGAAGCTACCGTAGAACGGTa < 1:962957/71‑1 (MQ=255)
aaGAACCGGGTAAAAACCATCCGCCATATCACCACCGTCATCACGCAGCGTGAAGCTACCGTAGAACGGTa < 1:1413882/71‑1 (MQ=255)
aaGAACCGGGTAAAAACCATCCGCCATATCACCACCGTCATCACGCAGCGTGAAGCCACCGTAGAACgg > 1:1435803/1‑69 (MQ=255)
aaGAACCGGGTAAAAACCATCCGCCATATCACCACCGTCATCACGCAGCGTGAAGCCACCGTAGAACGGt > 1:2069593/1‑70 (MQ=255)
aGAACCGGGTAAAAACCATCCGCCATATCACCACCGTCATCACGCAGCGTGAAGCTACCGTAGAACGGTaa > 1:28628/1‑71 (MQ=255)
aaCCGGGTAAAAACCATCCGCCATATCACCACCGTCATCACGCAGCGTGAAGCTACCGTAGAACGGTAACt > 1:591088/1‑71 (MQ=255)
cGGGTAAAAACCATCCGCCATATCACCACCGTCATCACGCAGCGTGAAGCCACCGTAGAACGGTAACTGaa < 1:1360836/71‑1 (MQ=255)
cGGGTAAAAACCATCCGCCATATCACCACCGTCATCACGCAGCGTGAAGCCACCGTAGAACGGTAACTGaa < 1:744684/71‑1 (MQ=255)
gTAAAAACCATCCGCCATATCACCACCGTCATCACGCAGCGTGAAGCTACCGTAGAACGGTAACTGAACGt < 1:2428323/71‑1 (MQ=255)
tAAAAACCATCCGCCATATCACCACCGTCATCACGCAGCGTGAAGCCACCGTAGAACGGTaa > 1:247602/1‑62 (MQ=255)
aaaaCCATCCGCCATATCACCACCGTCATCACGCAGCGTGAAGCTACCGTAGAACGGTaa > 1:1938594/1‑60 (MQ=255)
aaaaCCATCCGCCATATCACCACCGTCATCACGCAGCGTGAAGCTACCGTAGAACGGTAACTGAACGt < 1:2751480/68‑1 (MQ=255)
aaaaCCATCCGCCATATCACCACCGTCATCACGCAGCGTGAAGCTAACGTAg > 1:1127922/1‑52 (MQ=255)
aaCCATCCGCCATATCACCACCGTCATCACGCAGCGTGAAGCTACCGTAGAACGGTAACTGAACGTaa > 1:1777934/1‑68 (MQ=255)
aaCCATCCGCCATATCACCACCGTCATCACGCAGCGTGAAGCTACCGTAGAACGGTAACTGAACGTaa > 1:2431213/1‑68 (MQ=255)
tCCGCCATATCACCACCGTCATCACGCAGCGTGAAGCTACCGTAGAACGGTAACTGAACGTAAGGCCCATa < 1:548511/71‑1 (MQ=255)
tCCGCCATATCACCACCGTCATCACGCAGCGTGAAGCCACCGTAGAACGGTAACTGAACGTAAGGCCCATa < 1:2430680/71‑1 (MQ=255)
tCCGCCATATCACCACCGTCATCACGCAGCGTGAAGCCACCGTAGAACGGTAACTGAACGTAAGGCCCATa < 1:1443344/71‑1 (MQ=255)
cGCCATATCACCACCGTCATCACGCAGCGTGAAGCTACCGTAGAACGGTAACTGAACGTAAGGCCCATAAc > 1:1758099/1‑71 (MQ=255)
cGCCATATCACCACCGTCATCACGCAGCGTGAAGCTACCGTAGAACGGTAACTGAACGTAAGGCCCATAAc > 1:457206/1‑71 (MQ=255)
gCCATATCACCACCGTCATCACGCAGCGTGAAGCCACCGTAGAACGGTAACTGAACGTAAGGCCCATAAcc < 1:701452/71‑1 (MQ=255)
ccATATCACCACCGTCATCACGCAGCGTGAAGCTAc < 1:2191737/36‑1 (MQ=255)
ccATATCACCACCGTCATCACGCAGCGTGAAGCCACCGTAGAACGGTAACTGAACGTAAGGCCCAt < 1:2458507/66‑1 (MQ=255)
cATATCACCACCGTCATCACGCAGCGTGAAGCTACCGTAGAACGGTAACTGAACGTAAGGCCCAt < 1:1715072/65‑1 (MQ=255)
cATATCACCACCGTCATCACGCAGCGTGAAGCTACCGTAGAACGGTAACTGAACGTAAGGCCCAt < 1:1101623/65‑1 (MQ=255)
atatCACCACCGTCATCACGCAGCGTGAAGCTACCGTAg < 1:149500/39‑1 (MQ=255)
atatCACCACCGTCATCACGCAGCGTGAAGCTACCGTAg < 1:610266/39‑1 (MQ=255)
atatCACCACCGTCATCACGCAGCGTGAAGCTACCGTAGAACGGTAACTGAACGTAAGGcc < 1:2444667/61‑1 (MQ=255)
tatCACCACCGTCATCACGCAGCGTGAAGCCACCGTAGAACGGt < 1:1574395/44‑1 (MQ=255)
atCACCACCGTCATCACGCAGCGTGAAGCCACCGTAGAACGGTaa > 1:1006320/1‑45 (MQ=255)
tCACCACCGTCATCACGCAGCGTGAAGCTACCGTAGAACGGTaa > 1:1712118/1‑44 (MQ=255)
tCACCACCGTCATCACGCAGCGTGAAGCTACCGTAGAACGGTAACTGAACGTAAGGCCCATAACCCACGc > 1:2718417/1‑70 (MQ=255)
tCACCACCGTCATCACGCAGCGTGAAGCCACCGTAGAACGGTAACTGAACGTAAGGCCCATAACCCACGc > 1:1717554/1‑70 (MQ=255)
tCACCACCGTCATCAAGCAGCGTGAAGCTACCGTAGaa > 1:256680/1‑38 (MQ=255)
caccacCGTCATCACGCAGCGTGAAGCTACCGTAGAACGGTAACTGAACGTAAGGCCCATAACCCACGCCa > 1:1919075/1‑71 (MQ=255)
caccacCGTCATCACGCAGCGTGAAGCTACCGTAGAACGGTAACTGAACGTAAGGCCCATAACCCACGCCa > 1:2617975/1‑71 (MQ=255)
accaccGTCATCACGCAGCGTGAAGCTACCGTAGAACGGTAACTGAACGTAAGGCCCATAACCCACGCCa < 1:832298/70‑1 (MQ=255)
accaccGTCATCACGCAGCGTGAAGCTACCGTAGAACGGTAACTGAACGTAAGGCCCATAACCCACGCCa > 1:51647/1‑70 (MQ=255)
accaccGTCATCACGCAGCGTGAAGCTACCGTAGAACGGTAACTGAACGTAAGGCCCATAACCCACGCCa > 1:454717/1‑70 (MQ=255)
accaccGTCATCACGCAGCGTGAAGCTACCGTAGAACGGTAACTGAACGTAAGGCCCATAACCCACGCCAt < 1:425128/71‑1 (MQ=255)
accaccGTCATCACGCAGCGTGAAGCTACCGTAGAACGGTAACTGAACGTAAGGCCCATAACCCACGCCAt < 1:1944725/71‑1 (MQ=255)
accaccGTCATCACGCAGCGTGAAGCTACCGTAGAACGGTAACTGAACGTAAGGCCCATAACCCACGCCAt < 1:2009260/71‑1 (MQ=255)
accaccGTCATCACGCAGCGTGAAGCCACCGTAGAACGGTAACTGaa > 1:2553204/1‑47 (MQ=255)
accGTCATCACGCAGCGTGAAGCTACCGTAGAACGGTAACTGAACGTAAGGcc > 1:1114041/1‑53 (MQ=255)
cGTCATCACGCAGCGTGAAGCTACCGTAGAACGGTAACTGAACGTAAGGCCCATaa > 1:2154971/1‑56 (MQ=255)
tcatcaCGCAGCGTGAAGCCACCGTAGAACGGTAACTGAACGTAAGGCCCATAACCCACGCCAt < 1:143102/64‑1 (MQ=255)
caCGCAGCGTGAAGCCACCGTAGAACGGTAACTGAACGTAAGGCCCATAACCCACGCCATAATGACCAAGc > 1:848214/1‑71 (MQ=255)
aCGCAGCGTGAAGCCACCGTAGAACGGTAACTGAACGTAAGGCCCATAACCCACGCCATAATGACCAAGCg < 1:164872/71‑1 (MQ=255)
aCGCAGCGTGAAGCCACCGTAGAACGGTAACTGAACGTAAGGCCCATAACCCACGCCATAATGACCAAGCg > 1:919040/1‑71 (MQ=255)
gCGTGAAGCTACCGTAGAACGGTAACTGAACGTAAGGCCCATAACCCACGCCAt < 1:1117480/54‑1 (MQ=255)
gCGTGAAGCCACCGTAGAACGGTAACTGAACGTAAGGCCCATAACCCACGCCAt < 1:24568/54‑1 (MQ=255)
aaGCTACCGTAGAACGGTAACTGAACGTAAGGCCCATAACCCACGCCATAATGACCAAGCGTACTACCg > 1:50355/1‑69 (MQ=255)
aaGCTACCGTAGAACGGTAACTGAACGTAAGGCCCATAACCCACGCCATAATGACCAAGCGTACTACCGa < 1:1909874/70‑1 (MQ=255)
aaGCCACCGTAGAACGGTAACTGAACGTAAGGCCCATACCCCACGCCATAATGa > 1:1811860/1‑54 (MQ=255)
aaGCCACCGTAGAACGGTAACTGAACGTAAGGCCCATAACCCACGCCATAATGa > 1:2171288/1‑54 (MQ=255)
cTACCGTAGAACGGTAACTGAACGTAAGGCCCATAACCCACGCCATAATGACCAAGCg < 1:1622119/58‑1 (MQ=255)
cTACCGTAGAACGGTAACTGAACGTAAGGCCCATAACCCACGCCATAATGACCAAGCg < 1:2387703/58‑1 (MQ=255)
cTACCGTAGAACGGTAACTGAACGTAAGACCCATAACCCACGCCATAATGACCAAGCg < 1:1329687/58‑1 (MQ=255)
|
CAGGAAAGAACCGGGTAAAAACCATCCGCCATATCACCACCGTCATCACGCAGCGTGAAGCTACCGTAGAACGGTAACTGAACGTAAGGCCCATAACCCACGCCATAATGACCAAGCGTACTACCGA > W3110S.gb/2469930‑2470056
|
| Alignment Legend |
|---|
Aligned base mismatch/match (shaded by quality score): ATCG/ATCG < 3 ≤ ATCG/ATCG < 21 ≤ ATCG/ATCG < 32 ≤ ATCG/ATCG < 36 ≤ ATCG/ATCG |
Unaligned base: atcg Masked matching base: atcg Alignment gap: ‑ Deleted base: ‑ |
GATK/CNVnator alignment
N/A
