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 R2
|
308 |
27.9 |
1975068 |
96.7% |
1909890 |
67.2 |
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 | 77.3%
| 102.0
/ 32.9
| 44 | coding (3964/4581 nt) | ypjA | adhesin‑like autotransporter |
| Reads supporting (aligned to +/- strand): ref base . (1/9); new base A (20/14); total (21/23) |
| Fisher's exact test for biased strand distribution p-value = 1.02e-02 |
| Kolmogorov-Smirnov test that lower quality scores support variant p-value = 9.87e-01 |
| Rejected as polymorphism: Variant not supported by required number of reads on each strand. |
| Rejected as polymorphism: Polymorphic indel expands or contracts a homopolymer stretch. |
ATGTTCCCAACTGGCATAGCCGCCCAGAGAATAACTGCCCACACTGCCATGTCCTCCGCGATC‑AAAACCGATATGTGAATGGGAATAGCCCATAAAAGCGCCTAGCGTGGTAATTCCTTCAG > W3110S.gb/2777357‑2777478
|
aTGTTCCCAACTGGCATAGCCTCCCAGAGAATAACTGCCCACACTGCCATGTCCTCCGCGATC‑AAAACCGa < 1:450641/71‑1 (MQ=255)
aTGTTCCCAACTGGCATAGCCGCCCAGAGAATAACTGCCCACACTGCCATGTCCTCCGCGATC‑AAAAccta < 1:1229113/71‑3 (MQ=255)
aTGTTCCCAACTGGCATAGCCGCCCAGAGAATAACTGCCCACACTGCCATGTCCTCCGCGATC‑AAAACCGa < 1:963684/71‑1 (MQ=255)
aTGTTCCCAACTGGCATAGCCGCCCAGAGAATAACTGCCCACACTGCCATGTCCTCCGCGATC‑AAAACCGa < 1:168839/71‑1 (MQ=255)
tGTTCCCAACTGGCATAGCCGCCCAGAGAATAACTTCCCACACTGCCATGTCCTCCGCGATC‑AAAACCGa < 1:1043617/70‑1 (MQ=255)
ttCCCAACTGGCATAGCCGCCCAGAGAATAACTGCCCACACTGCCATGTCCTCCGCGATCAAAAACCGata > 1:1915620/1‑71 (MQ=255)
cAACTGGCATAGCCGCCCAGAGAATAACTGCCCACACTGCCATGTCCTCCGCGATCAAAAACCGATAtgtg < 1:66202/71‑1 (MQ=255)
cAACTGGCATAGCCGCCCAGAGAATAACTGCCCACACTGCCATGTCCTCCGCGATCAAAAACCGATAtgtg < 1:272980/71‑1 (MQ=255)
cAACTGGCATAGCCGCCCAGAGAATAACTGCCCACACTGCCATGTCCTCCGCGATCAAAAACCGATAtgtg < 1:1625861/71‑1 (MQ=255)
gCATAGCCGCCCAGAGAATAACTGCCCACACTGCCATGTCCTCCGCGATC‑AAAACCGATATGTGAATggg < 1:1081888/70‑1 (MQ=255)
gCATAGCCGCCCAGAGAATAACTGCCCACACTGCCATGTCCTCCGCGATC‑AAAACCGATATGTGAATggg < 1:1223364/70‑1 (MQ=255)
gCATAGCCGCCCAGAGAATAACTGCCCACACTGCCATGTCCTCCGCGATC‑AAAACCGATATGTGAATggg < 1:464474/70‑1 (MQ=255)
cATAGCCGCCCAGAGAATAACTGCCCACACTGCCATGTCCTCCGCGATC‑AAAACCGATATGTGAATggg < 1:1699274/69‑1 (MQ=255)
gccgccCAGAGAATAACTGCCCACACTGCCATGTCCTCCGCGATCAAAAACCGATATGTGAATGGGAATAg > 1:290347/1‑71 (MQ=255)
gccgccCAGAGAATAACTGCCCACACTGCCATGTCCTCCGCGATCAAAAACCGATATGTGAATGGGAATAg > 1:194619/1‑71 (MQ=255)
gccgccCAGAGAATAACTGCCCACACTGCCATGTCCTCCGCGATCAAAAACCGATATGTGAATGGGAATAg > 1:1553976/1‑71 (MQ=255)
gccgccCAGAGAATAACTGCCCACACTGCCATGTCCTCCGCGATCAAAAACCGATATGTGAATGGGAATAg > 1:1455670/1‑71 (MQ=255)
cgccCAGAGAATAACTGCCCACACTGCCATGTCCTCCGCGATCAAAAACCGATATGTGAATGGGAATAGcc > 1:562162/1‑71 (MQ=255)
cgccCAGAGAATAACTGCCCACACTGCCATGTCCTCCGCGATCAAAAACCGATATGTGAATGGGAATAGcc > 1:884524/1‑71 (MQ=255)
cgccCAGAGAATAACTGCCCACACTGCCATGTCCTCCGCGATCAAAAACCGATATGTGAATGGGAATAGcc > 1:842639/1‑71 (MQ=255)
cgccCAGAGAATAACTGCCCACACTGCCATGTCCTCCGCGATCAAAAACCGATATGTGAATGGGAATAGcc > 1:465077/1‑71 (MQ=255)
cgccCAGAGAATAACTGCCCACACTGCCATGTCCTCCGCGATCAAAAACCGATATGTGAATGGGAATAGcc > 1:1965607/1‑71 (MQ=255)
cgccCAGAGAATAACTGCCCACACTGCCATGTCCTCCGCGATCAAAAACCGATATGTGAATGGGAATAGc > 1:1072100/1‑70 (MQ=255)
cgccCAGAGAATAACTGCCCACACTGCCATGTCCTCCGCGATCAAAAACCGATACGTGAATGGGAATAGcc > 1:813357/1‑71 (MQ=255)
tAACTGCCCACACTGCCATGTCCTCCGCGATCAAAAACCGATATGTGAATGGGAATAGCCCATAAAAgcgc > 1:1505218/1‑71 (MQ=255)
cacTGCCATGTCCTCCGCGATCAAAAACCGATATGTGAATGTGAATAGCCCATAAAAGCGCCTAGCGTGGt < 1:910851/71‑1 (MQ=255)
cacTGCCATGTCCTCCGCGATCAAAAACCGATATGTGAATGGGAATAGCCCATAAAAGCGCCTAGCGTGGt < 1:622556/71‑1 (MQ=255)
cacTGCCATGTCCTCCGCGATCAAAAACCGATATGTGAATGGGAATAGCCCATAAAAGCGCCTAGCGTGGt < 1:1904602/71‑1 (MQ=255)
cacTGCCATGTCCTCCGCGATCAAAAACCGATATGTGAATGGGAATAGCCCATAAAAGCGCCTAGCGTGGt < 1:816106/71‑1 (MQ=255)
cacTGCCATGTCCTCCGCGATCAAAAACCGATATGTGAATGGGAATAGCCCATAAAAGCGCCTAGCGTGGt < 1:801898/71‑1 (MQ=255)
cacTGCCATGTCCTCCGCGATCAAAAACCGATATGTGAATGGGAATAGCCCATAAAAGCGCCTAGCGTGGt < 1:726922/71‑1 (MQ=255)
cacTGCCATGTCCTCCGCGATCAAAAACCGATATGTGAATGGGAATAGCCCATAAAAGCGCCTAGCGTGGt < 1:598733/71‑1 (MQ=255)
cacTGCCATGTCCTCCGCGATCAAAAACCGATATGTGAATGGGAATAGCCCATAAAAGCGCCTAGCGTGGt < 1:569144/71‑1 (MQ=255)
cacTGCCATGTCCTCCGCGATCAAAAACCGATATGTGAATGGGAATAGCCCATAAAAGCGCCTAGCGTGGt < 1:437195/71‑1 (MQ=255)
cacTGCCATGTCCTCCGCGATCAAAAACCGATATGTGAATGGGAATAGCCCATAAAAGCGCCTAGCGTGGt < 1:434289/71‑1 (MQ=255)
acTGCCATGTCCTCCGCGATCAAAAACCGATATGTGAATGGGAATAGCCCATAAAAGCGCCTAGCGTGGt < 1:1381710/70‑1 (MQ=255)
gCCATGTCCTCCGCGATCAAAAACCGATATGTGAATGGGAATAGCCCATAAAAGCGCCTAGCGTGGTAAtt > 1:1643576/1‑71 (MQ=255)
aTGTCCTCCGCGATCAAAAACCGATATGTGAATGGGAATAGCCCATAAAAGCGCCTAGCGTGGTAATTCCt > 1:1530229/1‑71 (MQ=255)
aTGTCCTCCGCGATCAAAAACCGATATGTGAATGGGAATAGCCCATAAAAGCGCCTAGCGTGGTAATTCCt > 1:1400934/1‑71 (MQ=255)
tcctccGCGATCAAAAACCGATATGTGAATGGGAATAGCCCATAAAAGCGCCTAGCGTGGTAATTCCtt > 1:1149217/1‑69 (MQ=255)
tcctccGCGATCAAAAACCGATATGTGAATGGGAATAGCCCATAAAAGCGCCTAGCGTGGTAATTCCtt > 1:1340832/1‑69 (MQ=255)
tcctccGCGATCAAAAACCGATATGTGAATGGGAATAGCCCATAAAAGCGCCTAGCGTGGTAATTCCtt > 1:860912/1‑69 (MQ=255)
tcctccGCGATCAAAAACCGATATGTGAATGGGAATAGCCCATAAAAGCGCCTAGCGTGGTAATTCCtt > 1:408822/1‑69 (MQ=255)
tcctccGCGATC‑AAAACCGATATGTGAATGGGAATAGCCCATAAAAGCGCCTAGCGTGGTAATTCCTTCAg > 1:893642/1‑71 (MQ=255)
|
ATGTTCCCAACTGGCATAGCCGCCCAGAGAATAACTGCCCACACTGCCATGTCCTCCGCGATC‑AAAACCGATATGTGAATGGGAATAGCCCATAAAAGCGCCTAGCGTGGTAATTCCTTCAG > W3110S.gb/2777357‑2777478
|
| Alignment Legend |
|---|
Aligned base mismatch/match (shaded by quality score): ATCG/ATCG < 3 ≤ ATCG/ATCG < 32 ≤ ATCG/ATCG < 33 ≤ ATCG/ATCG < 36 ≤ ATCG/ATCG |
Unaligned base: atcg Masked matching base: atcg Alignment gap: ‑ Deleted base: ‑ |
GATK/CNVnator alignment
N/A
