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 |
|
A4 F1 I1 R1
|
765 |
39.6 |
1867486 |
94.4% |
1762906 |
108.0 |
Breseq alignment
BRESEQ :: Evidence
|
| evidence |
seq id |
position |
mutation |
annotation |
gene |
description |
| RA |
NC_000913 |
1,042,775 |
C→T |
R479H (CGC→CAC) |
etk ← |
tyrosine‑protein kinase, role in O‑antigen capsule formation |
|
| |
seq id |
position |
ref |
new |
freq |
score (cons/poly) |
reads |
annotation |
genes |
product |
| * | NC_000913 | 1,042,775 | 0 | C | T | 94.1%
| 44.8
/ ‑5.8
| 17 | R479H (CGC→CAC) | etk | tyrosine‑protein kinase, role in O‑antigen capsule formation |
| Reads supporting (aligned to +/- strand): ref base C (0/0); major base T (7/9); minor base A (1/0); total (8/9) |
| Fisher's exact test for biased strand distribution p-value = 4.71e-01 |
| Kolmogorov-Smirnov test that lower quality scores support variant p-value = 9.93e-01 |
TGCAGACTGGTTCGTAGCGCACGTACGGCTTCCACAGCAGAATCCGCCGGGTTATCCACCGCCAGGAAGGGGATATTTTTAGTACGATGGCGCTGCTGATTAGAAAATAAATTTTTCTTACGCAGACGGGTGCGTTTATCCAGCCACTCGGACATTGGGATAGTGGCATAAACGCTGATGCCGTGCTCTTCCAGTTGTTCCGGGGCTTCTACACCACGACGCAACATCGCACGCGCCAGCACGGCACC > NC_000913/1042643‑1042890
|
tGCAGACTGGTTCGTAGCGCACGTACGGCTTCCACAGCAGAATCCGCCGGGTTATCCACCGCCAGGAAGGGGATATTTTTAGTACGATGGCGCTGCTGATTAGAAAATAAATTTTTCTTACGCAGACGGGTGTGTTTAt > 2:822779/1‑139 (MQ=255)
aCGGCTTCCACAGCAGAATCCGCCGGGTTATCCACCGCCAGGAAGGGGATATTTTTAGTACGATGGCGCTGCTGATTAGAAAATAAATTTTTCTTACGCAGACGGGTGTGTTTATCCAGCCACTCGGACATTGGGATAg > 1:564144/1‑139 (MQ=255)
ccACAGCAGAATCCGCCGGGTTATCCACCGCCAGGAAGGGGATATTTTTAGTACGATGGCGCTGCTGATTAGAAAATAAATTTTTCTTACGCAGACGGGTGTGTTTATCCAGCCACTCGGACATTGGGATAGTGGCATa > 1:640513/1‑139 (MQ=255)
cGCCAGGAAGGGGATATTTTTAGTACGATGGCGCTGCTGATTAGAAAATAAATTTTTCTTACGCAGACGGGTGTGTTTATCCAGCCACTCGGACATTGGGATAGTgg < 2:223411/107‑1 (MQ=255)
cGCCAGGAAGGGGATATTTTTAGTACGATGGCGCTGCTGATTAGAAAATAAATTTTTCTTACGCAGACGGGTGAGTTTATCCAGCCACTCGGACATTGGGATAGTgg > 1:223411/1‑107 (MQ=255)
tGGCGCTGCTGATTAGAAAATAAATTTTTCTTACGCAGACGGGTGTGTTTATCCAGCCACTCGGACATTGGGATAGTGGCATAAACGCTGATGCCGTGCTCTTCCAGTTGTTCCGGGGc > 1:561080/1‑119 (MQ=255)
tGGCGCTGCTGATTAGAAAATAAATTTTTCTTACGCAGACGGGTGTGTTTATCCAGCCACTCGGACATTGGGATAGTGGCATAAACGCTGATGCCGTGCTCTTCCAGTTGTTCCGGGGc < 2:561080/119‑1 (MQ=255)
ctgctgATTAGAAAATAAATTTTTCTTACGCAGACGGGTGTGTTTATCCAGCCACTCGGACATTGGGATAGTGGCATAAACGCTGATGCCGTGCTCTTCCAGTTGTTCCGGGGCTTCTACACCACGACGCAACATCGCa < 1:310960/139‑1 (MQ=255)
ctgctgATTAGAAAATAAATTTTTCTTACGCAGACGGGTGTGTTTATCCAGCCACTCGGACATTGGGATAGTGGCATAAACGCTGATGCCGTGCTCTTCCAGTTGTTCCGGGGCTTCTACACCACGACGCAACATCGCa < 2:755666/139‑1 (MQ=255)
ctgctgATTAGAAAATAAATTTTTCTTACGCAGACGGGTGTGTTTATCCAGCCACTCGGACATTGGGATAGTGGCATAAACGCTGATGCCGTGCTCTTCCAGTTGTTCCGGGGCTTCTACACCACGACGCAACATCGCa < 1:783539/139‑1 (MQ=255)
ctgATTAGAAAATAAATTTTTCTTACGCAGACGGGTGTGTTTATCCAGCCACTCGGACATTGGGATAGTGGCATAAACGCTGATGCCGTGCTCTTCCAGTTGTTCCGGGGCTTCTACACCACGACGCAACATCGCAcgc > 1:679541/1‑139 (MQ=255)
aTTAGAAAATAAATTTTTCTTACGCAGACGGGTGTGTTTATCCAGCCACTCGGACATTGGGATAGTGGCATAAACGCTGATGCCGTGCTCTTCCAGTTGTTCCGGGGCTTCTACACCACGACGCAACATCGCACGCGcc < 1:822779/139‑1 (MQ=255)
aatTTTTCTTACGCAGACGGGTGTGTTTATCCAGCCACTCGGACATTGGGATAGTGGCATAAACGCTGATGCCGTGCTCTTCCAGTTGTTCCGGGGCTTCTACACCACGACGCAACATCGCACGCGCCAGCACGGCAcc < 1:423820/139‑1 (MQ=255)
aCGCAGACGGGTGTGTTTATCCAGCCACTCGGACATTGGGATAGTGGCATAAACGCTGATGCCGTGCTCTTCCAGTTGTTCCGGGGCTTc < 2:268673/90‑1 (MQ=255)
aCGCAGACGGGTGTGTTTATCCAGCCACTCGGACATTGGGATAGTGGCATAAACGCTGATGCCGTGCTCTTCCAGTTGTTCCGGGGCTTc > 1:268673/1‑90 (MQ=255)
aCGGGTGTGTTTATCCAGCCACTCGGACATTGGGATAGTGGCATAAACGCTGATGCCGTGc < 1:625879/61‑1 (MQ=255)
aCGGGTGTGTTTATCCAGCCACTCGGACATTGGGATAGTGGCATAAACGCTGATGCCGTGc > 2:625879/1‑61 (MQ=255)
|
TGCAGACTGGTTCGTAGCGCACGTACGGCTTCCACAGCAGAATCCGCCGGGTTATCCACCGCCAGGAAGGGGATATTTTTAGTACGATGGCGCTGCTGATTAGAAAATAAATTTTTCTTACGCAGACGGGTGCGTTTATCCAGCCACTCGGACATTGGGATAGTGGCATAAACGCTGATGCCGTGCTCTTCCAGTTGTTCCGGGGCTTCTACACCACGACGCAACATCGCACGCGCCAGCACGGCACC > NC_000913/1042643‑1042890
|
| Alignment Legend |
|---|
Aligned base mismatch/match (shaded by quality score): ATCG/ATCG < 3 ≤ ATCG/ATCG < 31 ≤ ATCG/ATCG < 36 ≤ ATCG/ATCG < 39 ≤ ATCG/ATCG < 40 ≤ ATCG/ATCG |
Unaligned base: atcg Masked matching base: atcg Alignment gap: ‑ Deleted base: ‑ |
GATK/CNVnator alignment
N/A
