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 |
|
A5 F21 I0 R2
|
316 |
65.6 |
5147759 |
97.4% |
5013917 |
60.3 |
Breseq alignment
BRESEQ :: Evidence
|
| evidence |
seq id |
position |
mutation |
freq |
annotation |
gene |
description |
| RA |
W3110S.gb |
3,764,664 |
T→C |
38.1% |
N106D (AAT→GAT) |
yidX ← |
predicted lipoproteinC |
|
| |
seq id |
position |
ref |
new |
freq |
score (cons/poly) |
reads |
annotation |
genes |
product |
| * | W3110S.gb | 3,764,664 | 0 | T | C | 38.1%
| 47.1
/ 70.9
| 63 | N106D (AAT→GAT) | yidX | predicted lipoproteinC |
| Reads supporting (aligned to +/- strand): ref base T (18/21); new base C (9/15); total (27/36) |
| Fisher's exact test for biased strand distribution p-value = 6.03e-01 |
| Kolmogorov-Smirnov test that lower quality scores support variant p-value = 7.32e-01 |
TTTCTTCTTCGTTATTCCAGTAGTAGTAAAGCGATATTGTGCCGGTAAATTTCTTTTTCCCCGCATTTAAAACAAATCTTGCGTCATCGGCAACCTGAATATTGTGCCGGTTAAGTGCTGGATCATTGAGCATCTT > W3110S.gb/3764598‑3764733
|
tttCTTCTTCGTTATTCCAGTAGTAGTAAAGCGATATTGTGCCGGTAAATTTCTTTTTCCCCGCATCTaa > 1:4912762/1‑70 (MQ=255)
ttcttcttcGTTATTCCAGTAGTAGTAAAGCGATATTGTGCCGGTAAATTTCTTTTTCCCCGCATTTaa < 1:1135931/69‑1 (MQ=255)
ttcttcttcGTTATTCCAGTAGTAGTAAAGCGATATTGTGCCGGTAAATTTCTTTTTCCCCGCATTTaa < 1:3940629/69‑1 (MQ=255)
ttcttcttcGTTATTCCAGTAGTAGTAAAGCGATATTGTGCCGGTAAATTTCTTTTTCCCCGCATTTaa < 1:2604159/69‑1 (MQ=255)
cGTTATTCCAGTAGTAGTAAAGCGATATTGTGCCGGTAAATTTCTTTTTCCCCGCATCTAAAACAAAt < 1:4569885/68‑1 (MQ=255)
aTTCCAGTAGTAGTAAAGCGATATTGTGCCGGTAAATTTCTTTTTCCCCGCATTTAAAACAAATCTTGCg < 1:4363146/70‑1 (MQ=255)
aTTCCAGTAGTAGTAAAGCGATATTGTGCCGGTAAATTTCTTTTTCCCCGCATTTAAAACAAATCTTGCGt > 1:3847576/1‑71 (MQ=255)
aTTCCAGTAGTAGTAAAGCGATATTGTGCCGGTAAATTTCTTTTTCCCCGCATTTAAAACAAATCTTGCGt > 1:129392/1‑71 (MQ=255)
aTTCCAGTAGTAGTAAAGCGATATTGTGCCGGTAAATTTCTTTTTCCCCGCATTTAAAACAAATCTTGCGt > 1:568855/1‑71 (MQ=255)
ccAGTAGTAGTAAAGCGATATTGTGCCGGTAAATTTCTTTTTCCCCGCATTTAAAACAAATCTTGCGTCa < 1:4289164/70‑1 (MQ=255)
cAGTAGTAGTAAAGCGATATTGTGCCGGTAAATTTCTTTTTCCCCGCATTTAAAACAAATCTTGCGTCAt < 1:3887810/70‑1 (MQ=255)
cAGTAGTAGTAAAGCGATATTGTGCCGGTAAATTTCTTTTTCCCCGCATTTAAAACAAATCTTGCGTCAt < 1:4032389/70‑1 (MQ=255)
tagtaAAGCGATATTGTGCCGGTAAATTTCTTTTTCCCCGCATTTAAAACAAATCtt < 1:3819910/57‑1 (MQ=255)
tagtaAAGCGATATTGTGCCGGTAAATTTCTTTTTCCCCGCATCTAAAACAAAt < 1:2510125/54‑1 (MQ=255)
tagtaAAGCGATATTGTGCCGGTAAATTTCTTTTTCCCCGCATCTAAAACAAAt < 1:287712/54‑1 (MQ=255)
gtaAAGCGATATTGTGCCGGTAAATTTCTTTTTCCCCGCATTTAAAACAAATCTTGCGTCATCGGCAAc > 1:4266555/1‑69 (MQ=255)
gtaAAGCGATATTGTGCCGGTAAATTTCTTTTTCCCCGCATTTAAAACAAATCTTGCGTCATCGGCAACCt > 1:4728051/1‑71 (MQ=255)
gtaAAGCGATATTGTGCCGGTAAATTTCTTTTTCCCCGCATTTAAAACAAATCTTGCGTCATCGGCAACCt > 1:4045141/1‑71 (MQ=255)
aaaGCGATATTGTGCCGGTAAATTTCTTTTTCCCCGCATTTaa < 1:2775939/43‑1 (MQ=255)
aaaGCGATATTGTGCCGGTAAATTTCTTTTTCCCCGCATTTAAAACAAATCTTGCGTCAt > 1:2747561/1‑60 (MQ=255)
aaaGCGATATTGTGCCGGTAAATTTCTTTTTCCCCGCATTTAAAACAAATCTTGCGTCATCGGCAACCTg > 1:1721491/1‑70 (MQ=255)
aaGCGATATTGTGCCGGTAAATTTCTTTTTCCCCGCATTTAAAACGAATCTTGCGTCATCGGCAACCTGaa > 1:4666359/1‑71 (MQ=255)
aaGCGATATTGTGCCGGTAAATTTCTTTTTCCCCGCATCTAAAACAAATCTTGCg > 1:2934528/1‑55 (MQ=255)
gCGATATTGTGCCGGTAAATTTCTTTTTCCCCGCATTTAAAACAAATCTTGCGTCATCGGCAACCTGAata > 1:960707/1‑71 (MQ=255)
atatTGTGCCGGTAAATTTCTTTTTCCCCGCATTTAAAACAAATCTTGCGTCATCGGCAACCTGAATATtg < 1:534224/71‑1 (MQ=255)
tatTGTGCCGGTAAATTTCTTTTTCCCCGCATTTAAAACAAATCTTGCGTCATCGGCAACCTGAATATtgt < 1:4928957/71‑1 (MQ=255)
tatTGTGCCGGTAAATTTCTTTTTCCCCGCATTTAAAACAAATCTTGCGTCATCGGCAACCTGAATATtgt < 1:950509/71‑1 (MQ=255)
tatTGTGCCGGTAAATTTCTTTTTCCCCGCATTTAAAACAAATCTTGCGTCATCGGCAACCTGAATATtgt < 1:758249/71‑1 (MQ=255)
tatTGTGCCGGTAAATTTCTTTTTCCCCGCATCTAAAACAAATCTTGCGTCATCGGCAACCTGAATATtgt < 1:4323114/71‑1 (MQ=255)
tatTGTGCAGGTAAATTTCTTTTTCCCCGCATTTAAAACAAATCTTGCGTCATCGGCAACCTGAATATtgt < 1:990010/71‑1 (MQ=255)
atTGTGCCGGTAAATTTCTTTTTCCCCGCATTTAAAACAAATCTTGCGTCATCGGCAACCTGAATAtt > 1:578876/1‑68 (MQ=255)
atTGTGCCGGTAAATTTCTTTTTCCCCGCATCTAAAACAAATCTTGCGTCATCGGCAACCTGAATATtgtg > 1:976222/1‑71 (MQ=255)
ttGTGCCGGTAAATTTCTTTTTCCCCGCATTTAAAACaa < 1:1824098/39‑1 (MQ=255)
ttGTGCCGGTAAATTTCTTTTTCCCCGCATCTAAAACAAATCTTGCGTCATCGGCAACCTg < 1:1129082/61‑1 (MQ=255)
ttGTGCCGGTAAATTTCTTTTTCCCCGCATCTAAAACAAATCTTGCGTCATCGGCAACCTg < 1:2431211/61‑1 (MQ=255)
gtgCCGGTAAATTTCTTTTTCCCCGCATTTAAAACAAATCTTGCGTCATCGGCAACCTGAATATTGTGCCg > 1:442508/1‑71 (MQ=255)
gtgCCGGTAAATTTCTTTTTCCCCGCATCTAAAACAAATCTTGCGTCATCGGCAACCTGaa > 1:3478242/1‑61 (MQ=255)
cGGTAAATTTCTTTTTCCCCGCATTTAAAACAAATCTTGCGTCATCGGCAACCTGAATATTGTGCCGGTTa < 1:3257930/71‑1 (MQ=255)
cGGTAAATTTCTTTTTCCCCGCATCTAAAACAAATCTTGCGTCATCGGCAACCTGAATATTGTGCCGGTTa < 1:49313/71‑1 (MQ=255)
cGGTAAATTTCTTTTTCCCCGCATCTAAAACAAATCTTGCGTCATCGGCAACCTGAATATTGTGCCGGTTa < 1:3925667/71‑1 (MQ=255)
gTAAATTTCTTTTTCCCCGCATCTAAAACAAATCTTGCGTCATCGGCAAc > 1:1131987/1‑50 (MQ=255)
gTAAATTTCTTTTTCCCCGCATCTAAAACAAATCTTGCGTCATCGGCAAc > 1:1457477/1‑50 (MQ=255)
gTAAATTTCTTTTTCCCCGCATCTAAAACAAATCTTGCGTCATCGGCAACCTGAATATTGTGCCGGTTAAg < 1:3177544/71‑1 (MQ=255)
tAAATTTCTTTTTCCCCGCATCTAAAACAAATCTTGCGTCATCGGCAACCTGAATATTGTGCCGGtt < 1:4820998/67‑1 (MQ=255)
tAAATTTCTTTTTCCCCGCATCTAAAACAAATCTTGCGTCATCGGCAACCTGAATATTGTGCCGGtt < 1:1276332/67‑1 (MQ=255)
aaaaTATCTTTTTCCCCGCATCTAAAACAAATCTTGCGTCATCGGCAACCTGAATATTGTGCCGGtt < 1:1157293/66‑1 (MQ=255)
aaaTTTCTTTTTCCCCGCATTTAAAACAAATCTTGCGTCATCGGCaa > 1:3275700/1‑47 (MQ=255)
aaaTTTCTTTTTCCCCGCATTTAAAACAAATCTTGCGTCATCGGCAAGCTGAata > 1:1678989/1‑55 (MQ=255)
aaaTTTCTTTTTCCCCGCATTTAAAACAAATCTTGCGACATCGGCAACCTGAATATTGTGCCGGTTAAGTg > 1:2769619/1‑71 (MQ=255)
aaTTTCTTTTTCCCCGCATTTAAAACAAATCTTGCGTCATCGGc > 1:1515398/1‑44 (MQ=255)
aaTTTCTTTTTCCCCGCATCTAAAACAAATCTTGCGTCATCGGCAAc > 1:4427790/1‑47 (MQ=255)
aTTTCTTTTTCCCCGCATTTAAAACAAATCTTGCGTCa < 1:2698564/38‑1 (MQ=255)
aTTTCTTTTTCCCCGCATTTAAAACAAATCTTGCGTCATCGGCAACCTGAATAtt < 1:2476260/55‑1 (MQ=255)
aTTTCTTTTTCCCCGCATCTAAAACAAATCTTGCGTCATCGGCAACCTGAatat < 1:4636607/54‑1 (MQ=255)
tCTTTTTCCCCGCATCTAAAACAAATCTTGCGTCa > 1:4708781/1‑35 (MQ=255)
cTTTTTCCCCGCATCTAAAACAAATCTTGCGTCAt < 1:2882631/35‑1 (MQ=255)
tttCCCCGCATTTAAAACAAATCTTGCGTCATCGGCAACCTGaa > 1:3577000/1‑44 (MQ=255)
tttCCCCGCATTTAAAACAAATCTTGCGTCATCGGCAACCTGAATATTGTGCCGGTTAAGTGCTGGATCa < 1:3677220/70‑1 (MQ=255)
tttCCCCGCATCTAAAACAAATCTTGCGTCATCGGCAACCTGAATATTGTGc > 1:4801769/1‑52 (MQ=255)
ttCCCCGCATTTAAAACAAATCTTGCGTCATCGGCAACCTGAATATTGTGCCGGTTAAGTGCTGGATCAt < 1:3380851/70‑1 (MQ=255)
cccGCATTTAAAACAAATCTTGCGTCATCGGCAACCTGAATATTGTGCCGGTTAAGTGCTGGATCATTGAg < 1:612140/71‑1 (MQ=255)
ccGCATCTAAAACAAATCTTGCGTCATCGGCAACCTGAATATTGTGCCGGTTAAGTGCTGGATCATTGAGc < 1:2387516/71‑1 (MQ=255)
cATTTAAAACAAATCTTGCGTCATCGGCAACCTGAATATTGTGCCGGTTAAGTGCTGGATAATTGAGCATc > 1:914448/1‑71 (MQ=255)
ttAAAACAAATCTTGCGTCATCGGCAACCTGAATATTGTGCCGGTTAAGTGCTGGATCATTGAGCATCtt > 1:4964182/1‑70 (MQ=255)
ttAAAACAAATCTTGCGTCATCGGCAACCTGAATATTGTGCCGGTTAAGTGCTGGATCATTGAGCATCtt > 1:4403289/1‑70 (MQ=255)
|
TTTCTTCTTCGTTATTCCAGTAGTAGTAAAGCGATATTGTGCCGGTAAATTTCTTTTTCCCCGCATTTAAAACAAATCTTGCGTCATCGGCAACCTGAATATTGTGCCGGTTAAGTGCTGGATCATTGAGCATCTT > W3110S.gb/3764598‑3764733
|
| 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
