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 F28 I2 R2
|
154 |
32.4 |
3140800 |
76.4% |
2399571 |
54.5 |
Breseq alignment
BRESEQ :: Evidence
|
| evidence |
seq id |
position |
mutation |
annotation |
gene |
description |
| RA |
W3110S.gb |
1,141,889 |
(A)6→7 |
coding (280/954 nt) |
flgL → |
flagellar hook‑filament junction protein |
|
| |
seq id |
position |
ref |
new |
freq |
score (cons/poly) |
reads |
annotation |
genes |
product |
| * | W3110S.gb | 1,141,883 | 1 | . | A | 77.8%
| 16.1
/ 2.1
| 9 | coding (274/954 nt) | flgL | flagellar hook‑filament junction protein |
| Reads supporting (aligned to +/- strand): ref base . (2/0); new base A (7/0); total (9/0) |
| Fisher's exact test for biased strand distribution p-value = 1.00e+00 |
| Kolmogorov-Smirnov test that lower quality scores support variant p-value = 1.00e+00 |
ACTTAGCCAGGTCACCACTGCTATCCAGAATGCTCAGG‑AAAAAATTGTCTACGCCAGCAATGGCA > W3110S.gb/1141846‑1141910
|
aCTTAGCCAGGTCACCACTGCTATCCAGAATGCTCAGGAAAAAAATTGTCTACGCCAGCAAt > 1:1152713/1‑62 (MQ=255)
aCTTAGCCAGGTCACCACTGCTATCCAGAATGCTCAGGAAAAAAATTGTCTACGCCAGCAAt > 1:1851578/1‑62 (MQ=255)
aCTTAGCCAGGTCACCACTGCTATCCAGAATGCTCAGGAAAAAAATTGTCTACGCCAGCAAt > 1:2017011/1‑62 (MQ=255)
aCTTAGCCAGGTCACCACTGCTATCCAGAATGCTCAGGAAAAAAATTGTCTACGCCAGCAAt > 1:2855836/1‑62 (MQ=255)
aCTTAGCCAGGTCACCACTGCTATCCAGAATGCTCAGGAAAAAAATTGTCTACGCCAGCAAt > 1:3074948/1‑62 (MQ=255)
aCTTAGCCAGGTCACCACTGCTATCCAGAATGCTCAGGAAAAAAATTGTCTACGCCAGCAAt > 1:971579/1‑62 (MQ=255)
aCTTAGCCAGGTCACCACTGCTATCCAGAATGCTCAGGAAAAAAATTGTCTACGCCAGCAAt > 1:974159/1‑62 (MQ=255)
tAGCCAGGTCACCACTGCTATCCAGAATGCTCAGG‑AAAAAATTGTCTACGCCAGCAATGGCa > 1:1385982/1‑62 (MQ=255)
tAGCCAGGTCACCACTGCTATCCAGAATGCTCAGG‑AAAAAATTGTCTACGCCAGCAATGGCa > 1:1578546/1‑62 (MQ=255)
|
ACTTAGCCAGGTCACCACTGCTATCCAGAATGCTCAGG‑AAAAAATTGTCTACGCCAGCAATGGCA > W3110S.gb/1141846‑1141910
|
| Alignment Legend |
|---|
Aligned base mismatch/match (shaded by quality score): ATCG/ATCG < 3 ≤ ATCG/ATCG < 27 ≤ ATCG/ATCG < 32 ≤ ATCG/ATCG < 36 ≤ ATCG/ATCG |
Unaligned base: atcg Masked matching base: atcg Alignment gap: ‑ Deleted base: ‑ |
GATK/CNVnator alignment
N/A
