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 F17 I0 R2
|
276 |
45.3 |
3729697 |
93.0% |
3468618 |
60.6 |
Breseq alignment
BRESEQ :: Evidence
|
| evidence |
seq id |
position |
mutation |
freq |
annotation |
gene |
description |
| RA |
W3110S.gb |
2,777,419:1 |
+A |
100% |
coding (3964/4581 nt) |
ypjA ← |
adhesin‑like autotransporter |
|
| |
seq id |
position |
ref |
new |
freq |
score (cons/poly) |
reads |
annotation |
genes |
product |
| * | W3110S.gb | 2,777,419 | 1 | . | A | 86.7%
| 115.1
/ 15.9
| 45 | coding (3964/4581 nt) | ypjA | adhesin‑like autotransporter |
| Reads supporting (aligned to +/- strand): ref base . (2/4); new base A (10/29); total (12/33) |
| Fisher's exact test for biased strand distribution p-value = 6.50e-01 |
| Kolmogorov-Smirnov test that lower quality scores support variant p-value = 9.40e-01 |
| Rejected as polymorphism: Polymorphic indel expands or contracts a homopolymer stretch. |
TTCATGTTCCCAACTGGCATAGCCGCCCAGAGAATAACTGCCCACACTGCCATGTCCTCCGCGATC‑AAAACCGATATGTGAATGGGAATAGCCCATAAAAGCGCCTAGCGTGGTAATTCCTTCAGGAATATC > W3110S.gb/2777354‑2777485
|
ttCATGTTCCCAACTGGCATAGCCGCCCAGAGAATAACTGCCCACACTGCCATGTCCTCCGCGATC‑aaa > 1:2811165/1‑69 (MQ=255)
tCATGTTCCCAACTGGCATAGCCGCCCAGAGAATAACTGCCCACACTGCCATGTCCTCCGCGATC‑aaa > 1:2142565/1‑68 (MQ=255)
cATGTTCCCAACTGGCATAGCCGCCCAGAGAATAACTGCCCACACTGCCATGTCCTCCGCGATC‑aaaa > 1:2800152/1‑68 (MQ=255)
aTGTTCCCAACTGGCATAGCCGCCCAGAGAATAACTGCCCACACTGCCATGTCCTCCGCGATC‑aaaaa > 1:3284173/1‑67 (MQ=255)
aTGTTCCCAACTGGCATAGCCGCCCAGAGAATAACTGCCCACACTGCCATGTCCTCCGCGATC‑aaaaa > 1:2067013/1‑67 (MQ=255)
aTGTTCCCAACTGGCATAGCCGCCCAGAGAATAACTGCCCACACTGCCATGTCCTCCGCGATC‑aaaa < 1:1563876/67‑1 (MQ=255)
tGTTCCCAACTGGCATAGCCGCCCAGAGAATAACTGCCCACACTGCCATGTCCTCCGCGATC‑aaaaac < 1:1852333/68‑3 (MQ=255)
tGTTCCCAACTGGCATAGCCGCCCAGAGAATAACTGCCCACACTGCCATGTCCTCCGCGATC‑aaaaac < 1:1930606/68‑3 (MQ=255)
gTTCCCAACTGGCATAGCCGCCCAGAGAATAACTGCCCACACTGCCATGTCCTCCGCGATC‑AAAACCGa < 1:1424397/69‑1 (MQ=255)
ttCCCAACTGGCATAGCCGCCCAGAGAATAACTGCCCACACTGCCATGTCCTCCGCGATC‑a > 1:2934341/1‑61 (MQ=255)
aaCTGGCATAGCCGCCCAGAGAATAACTGCCCACACTGCCATGTCCTCCGCGATC‑AAAACCGATAtgtg < 1:173066/69‑1 (MQ=255)
aCTGGCATAGCCGCCCAGAGAATAACTGCCCACACTGCCATGTCCTCCGCGATCAAAAACCGATAtgtg < 1:465049/69‑1 (MQ=255)
aCTGGCATAGCCGCCCAGAGAATAACTGCCCACACTGCCATGTCCTCCGCGATCAAAAACCGATAtgtg < 1:1494336/69‑1 (MQ=255)
aCTGGCATAGCCGCCCAGAGAATAACTGCCCACACTGCCATGTCCTCCGCGATCAAAAACCGATAtgtg < 1:1762877/69‑1 (MQ=255)
aTAGCCGCCCAGAGAATAACTGCCCACACTGCCATGTCCTCCGCGATCAAAAACCGATATGTGAATg < 1:2230108/67‑1 (MQ=255)
aTAGCCGCCCAGAGAATAACTGCCCACACTGCCATGTCCTCCGCGATCAAAAACCGATATGTGAATg < 1:1713309/67‑1 (MQ=255)
aTAGCCGCCCAGAGAATAACTGCCCACACTGCCATGTCCTCCGCGATCAAAAACCGATATGTGAATg < 1:118983/67‑1 (MQ=255)
tAGCCGCCCAGAGAATAACTGCCCACACTGCCATGTCCTCCGCGATCAAAAACCGATATGTGAATg < 1:3653466/66‑1 (MQ=255)
tAGCCGCCCAGAGAATAACTGCCCACACTGCCATGTCCTCCGCGATCAAAAACCGATATGTGAATGGGa < 1:3174470/69‑1 (MQ=255)
tAGCCGCCCAGAGAATAACTGCCCACACTGCCATGTCCTCCGCGATCAAAAACCGATATGTGAATGGGa < 1:2614926/69‑1 (MQ=255)
gccgccCAGAGAATAACTGCCCACACTGCCATGTCCTCCGCGATCAAAAACCGATAtgtg < 1:3542582/60‑1 (MQ=255)
cAGAGAATAACTGCCCACACTGCCATGTCCTCCGCGATCAAAAACCGATATGTGAATggg > 1:3238376/1‑60 (MQ=255)
cAGAGAATAACTGCCCACACTGCCATGTCCTCCGCGATCAAAAACCGATATGTGAATggg > 1:202616/1‑60 (MQ=255)
gaATAACTGCCCACACTGCCATGTCCTCCGCGATCAAAAACCGATAtgtg < 1:2455141/50‑1 (MQ=255)
gaATAACTGCCCACACTGCCATGTCCTCCGCGATCAAAAACCGATAtgtg < 1:3659112/50‑1 (MQ=255)
gaATAACTGCCCACACTGCCATGTCCTCCGCGATCAAAAACCGATAtgtg < 1:2708942/50‑1 (MQ=255)
gaATAACTGCCCACACTGCCATGTCCTCCGCGATCAAAAACCGATATGTGAATGGGAATAGCCCATaaa > 1:2451976/1‑69 (MQ=255)
aaTAACTGCCCACACTGCCATGTCCTCCGCGATC‑AAAACCGATATGTGAATGGGAATAGCCCATAAAAg > 1:15855/1‑69 (MQ=255)
aCTGCCCACACTGCCATGTCCTCCGCGATCAAAAACCGATATGTGAATggg < 1:2162677/51‑1 (MQ=255)
aCTGCCCACACTGCCATGTCCTCCGCGATCAAAAACCGATATGTGAATggg < 1:269259/51‑1 (MQ=255)
aCTGCCCACACTGCCATGTCCTCCGCGATCAAAAACCGATATGTGAATggg < 1:1207182/51‑1 (MQ=255)
cTGCCCACACTGCCATGTCCTCCGCGATCAAAAACCGATATGTGAATGGGAATAGCCCATaaa > 1:3172732/1‑63 (MQ=255)
cTGCCCACACTGCCATGTCCTCCGCGATCAAAAACCGATATGTGAATGGGAATAGCCCATaaa > 1:701123/1‑63 (MQ=255)
cTGCCATGTCCTCCGCGATCAAAAACCGATAtgtg < 1:1073237/35‑1 (MQ=37)
cTGCCATGTCCTCCGCGATCAAAAACCGATAtgtg < 1:3405133/35‑1 (MQ=37)
cTGCCATGTCCTCCGCGATCAAAAACCGATAtgtg > 1:3195683/1‑35 (MQ=37)
cTGCCATGTCCTCCGCGATCAAAAACCGATATGTGAATGGGAATAGCCCATAAAAGCGCCTAGCGTGGt < 1:3678702/69‑1 (MQ=255)
tGCCATGTCCTCCGCGATCAAAAACCGATATGTGAATGGGAATAGCCCATAAAAGCGCCTAGCGTGGt < 1:663140/68‑1 (MQ=255)
tGCCATGTCCTCCGCGATCAAAAACCGATATGTGAATGGGAATAGCCCATAAAAGCGCCTAGCGTGGt > 1:898781/1‑68 (MQ=255)
ccATGTCCTCCGCGATCAAAAACCGATATGTGAATggg < 1:3128908/38‑1 (MQ=38)
ccATGTCCTCCGCGATCAAAAACCGATATGTGAATggg < 1:2686176/38‑1 (MQ=38)
ccATGTCCTCCGCGATCAAAAACCGATATGTGAATggg < 1:732309/38‑1 (MQ=38)
ctGTCCTCCGCGATCAAAAACCGATATGTGAATGGGAATAGCCCATAAAAGCGCCTAGCGTGGTAAt < 1:1964948/66‑1 (MQ=255)
aTGTCCTCCGCGATCAAAAACCGATATGTGAATGGGAATAGCCCATAAAAGCGCCTAGCGTGGTAAt < 1:1470763/67‑1 (MQ=255)
aTGTCCTCCGCGATCAAAAACCGATATGTGAATGGGAATAGCCCATAAAAGCGCCTAGCGTGGTAAt < 1:2145982/67‑1 (MQ=255)
tcctccGCGATCAAAAACCGATATGTGAATGGGAATAGCCCATa > 1:3188072/1‑44 (MQ=38)
tcctccGCGATCAAAAACCGATATGTGAATGGGAATAGCCCATa > 1:494145/1‑44 (MQ=38)
ctccGCGATCAAAAACCGATATGTGAATGGGAATAGCCCATAAAAGCGCCTAGCGTGGTAATTCCTTc < 1:684843/68‑1 (MQ=255)
cgcgATCAAAAACCGATATGTGAATGGGAATAGCCCATAAAAGCGCCTAGCGTGGTAATTCCTTCAgg > 1:1400860/1‑68 (MQ=255)
cgATCAAAAACCGATATGTGAATGGGAATAGCCCATAAAAGCGCCTAGCGTGGTAATTCCTTCAgg < 1:2452238/66‑1 (MQ=255)
cgATCAAAAACCGATATGTGAATGGGAATAGCCCATAAAAGCGCCTAGCGTGGTAATTCCTTCAgg < 1:2334426/66‑1 (MQ=255)
gATC‑AAAACCGATATGTGAATGGGAATAGCCCATAAAAGCGCCTAGCGTGGTAATTCCTTCAGGAatat < 1:437714/69‑1 (MQ=255)
gATC‑AAAACCGATATGTGAATGGGAATAGCCCATAAAAGCGCCTAGCGTGGTAATTCCTTCAGGAatat < 1:2381317/69‑1 (MQ=255)
tC‑AAAACCGATATGTGAATGGGAATAGCCCATAAAAGCGCCTAGCGTGGTAATTCCTTCAGGAATATc > 1:2211752/1‑68 (MQ=255)
|
TTCATGTTCCCAACTGGCATAGCCGCCCAGAGAATAACTGCCCACACTGCCATGTCCTCCGCGATC‑AAAACCGATATGTGAATGGGAATAGCCCATAAAAGCGCCTAGCGTGGTAATTCCTTCAGGAATATC > W3110S.gb/2777354‑2777485
|
| 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
