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 |
4,501,500 |
A→G |
83.0% |
Q23Q (CAA→CAG) |
intB → |
predicted integrase |
|
| |
seq id |
position |
ref |
new |
freq |
score (cons/poly) |
reads |
annotation |
genes |
product |
| * | W3110S.gb | 4,501,500 | 0 | A | G | 83.0%
| 130.1
/ 18.1
| 53 | Q23Q (CAA→CAG) | intB | predicted integrase |
| Reads supporting (aligned to +/- strand): ref base A (2/7); new base G (19/25); total (21/32) |
| Fisher's exact test for biased strand distribution p-value = 2.91e-01 |
| Kolmogorov-Smirnov test that lower quality scores support variant p-value = 8.84e-01 |
CATCTGCTTGTCCATCCAAATGGTTCTAAGTACTGGCGTTTGCAGTACCGTTATGAGGGAAAGCAAAAAATGCTGGCACTTGGGGTTTATCCTGAAATCACACTAGCGGATGCCAGAGT > W3110S.gb/4501435‑4501553
|
cATCTGCTTGTCCATCCAAATGGTTCTAAGTACTGGCGTTTGCAGTACCGTTATGAGGGAAAGCaaaa < 1:2747933/68‑1 (MQ=255)
cATCTGCTTGTCCATCCAAATGGTTCTAAGTACTGGCGTTTGCAGTACCGTTATGAGGGAAAGCaaaa < 1:1783452/68‑1 (MQ=255)
aTCTGCTTGTCCATCCAAATGGTTCTAAGTACTGGCGTTTGCAGTACCGTTATGAGGGAAAGCaaaa < 1:1554508/67‑1 (MQ=255)
tGCTTGTCCATCCAAATGGTTCTAAGTACTGGCGTTTGCAGTACCGTTATGAGGGAAAGCAGAAAATGc > 1:2627235/1‑69 (MQ=255)
tGCTTGTCCATCCAAATGGTTCTAAGTACTGGCGTTTGCAGTACCGTTATGAGGGAAAGCAGAAAATGc > 1:1488589/1‑69 (MQ=255)
tGCTTGTCCATCCAAATGGTTCTAAGTACTGGCGTTTGCAGTACCGTTATGAGGGAAAGCAGAAAATGc > 1:1871793/1‑69 (MQ=255)
gCTTGTCCATCCAAATGGTTCTAAGTACTGGCGTTTGCAGTACCGTTATGAGGGAAAGCAGAAAATg > 1:129241/1‑67 (MQ=255)
gCTTGTCCATCCAAATGGTTCTAAGTACTGGCGTTTGCAGTACCGTTATGAGGGAAAGCAGAAAATg > 1:1284730/1‑67 (MQ=255)
gCTTGTCCATCCAAATGGTTCTAAGTACTGGCGTTTGCAGTACCGTTATGAGGGAAAGCAAAAAATGCt > 1:170948/1‑69 (MQ=255)
cTTGTCCATCCAAATGGTTCTAAGTACTGGCGTTTGCAGTACCGTTATGAGGGAAAGCAGAAAATGCt > 1:2489424/1‑68 (MQ=255)
catccaAATGGTTCTAAGTACTGGCGTTTGCAGTACCGTTATGAGGGAAAGCagaaa < 1:2064417/57‑1 (MQ=255)
cataTGGTTCTAAGTACTGGCGTTTGCAGTACCGTTATGAGGGAAAGCAGAAAATGCTGGCACTTgggg < 1:2589894/66‑1 (MQ=255)
caAATGGTTCTAAGTACTGGCGTTTGCAGTACCGTTATGAGGGAAAGCAGAAAATGCTGGCACTTgggg > 1:1811551/1‑69 (MQ=255)
caAATGGTTCTAAGTACTGGCGTTTGCAGTACCGTTATGAGGGAAAGCAAAAAATGCTGGCACTTgggg > 1:3545836/1‑69 (MQ=255)
aTGGTTCTAAGTACTGGCGTTTGCAGTACCGTTATGAGGGAAAGCAGAAAATGCTgg < 1:1576625/57‑1 (MQ=255)
tGGTTCTAAGTACTGGCGTTTGCAGTACCGTTATGAGGGAAAGCAGAAAATGCTg > 1:887071/1‑55 (MQ=255)
tGGTTCTAAGTACTGGCGTTTGCAGTACCGTTATGAGGGAAAGCAGAAAATGCTGGCACTTGGGGTTTa > 1:634852/1‑69 (MQ=255)
cTAAGTACTGGCGTTTGCAGTACCGTTATGAGGGAAAGCAGAAAATGCTGGCACTTGGGGTTTATCCt > 1:3103309/1‑68 (MQ=255)
cTAAGTACTGGCGTTTGCAGTACCGTTATGAGGGAAAGCAGAAAATGCTGGCACTTGGGGTTTATCCTg < 1:1782824/69‑1 (MQ=255)
aaGTACTGGCGTTTGCAGTACCGTTATGAGGGAAAGCAAAAAATGCTGGCACTTGGGGTTTATCCTGa < 1:1623082/68‑1 (MQ=255)
aGTACTGGCGTTTGCAGTACCGTTATGAGGGAAAGCAGAAAAt < 1:1639918/43‑1 (MQ=255)
aGTACTGGCGTTTGCAGTACCGTTATGAGGGAAAGCAGAAAAt < 1:466796/43‑1 (MQ=255)
aGTACTGGCGTTTGCAGTACCGTTATGAGGGAAAGCAGAAAAt < 1:2255598/43‑1 (MQ=255)
aGTACTGGCGTTTGCAGTACCGTTATGAGGGAAAGCAGAAAAt < 1:2272820/43‑1 (MQ=255)
aGTACTGGCGTTTGCAGTACCGTTATGAGGGAAAGCAGAAAAt < 1:2310906/43‑1 (MQ=255)
aGTACTGGCGTTTGCAGTACCGTTATGAGGGAAAGCAGAAAAt < 1:483764/43‑1 (MQ=255)
tACTGGCGTTTGCAGTACCGTTATGAGGGAAAGCAGAAAATGCTGGCACTTGGGGTTTATCCTGAAAt < 1:1412241/68‑1 (MQ=255)
tACTGGCGTTTGCAGTACCGTTATGAGGGAAAGCAGAAAATGCTGGCACTTGGGGTTTATCCTGAAAt < 1:2026919/68‑1 (MQ=255)
tACTGGCGTTTGCAGTACCGTTATGAGGGAAAGCAGAAAATGCTGGCACTTGGGGTTTATCCTGAAAt < 1:874532/68‑1 (MQ=255)
aCTGGCTTTTGCAGTACCGTTATGAGGGAAAGCAGAAAATGc < 1:1419589/42‑1 (MQ=38)
aCTGGCGTTTGCAGTACCGTTATGAGGGAAAGCAGAAAATGc < 1:1400220/42‑1 (MQ=255)
aCTGGCGTTTGCAGTACCGTTATGAGGGAAAGCAGAAAATGc < 1:3260493/42‑1 (MQ=255)
aCTGGCGTTTGCAGTACCGTTATGAGGGAAAGCAAAAAATGCTGGCACTTGGGGTTTATCCTGAAATca < 1:3015882/69‑1 (MQ=255)
aCTGGCGTTTGCAGTACCGTTATGAGGGAAAGCAAAAAATGCTGGCACTTGGGGTTTATCCTGAAATca < 1:428766/69‑1 (MQ=255)
aCTGGCGTTTGCAGTACCGTTATGAGGGAAAGCAAAAAATGCTGGCACTTGGGGTTTATCCTGAAATca < 1:3438136/69‑1 (MQ=255)
cTGGCGTTTGCAGTACCGTTATGAGGGAAAGCAGAAAATGCTGGCACTTGGGGTTTATCCTGAAATca > 1:1454209/1‑68 (MQ=255)
cTGGCGTTTGCAGTACCGTTATGAGGGAAAGCAAAAAATGCTGGCACTTGGGGTTTATCCTGAAATcac < 1:3603470/69‑1 (MQ=255)
ggCGTTTGCAGTACCGTTATGAGGGAAAGCAGAAAAt < 1:2383315/37‑1 (MQ=255)
ggCGTTTGCAGTACCGTTATGAGGGAAAGCAGAAAAt < 1:2235682/37‑1 (MQ=255)
gCGTTTGCAGTACCGTTATGAGGGAAAGCaaaaaa < 1:2662226/35‑1 (MQ=255)
gCGTTTGCAGTACCGTTATGAGGGAAAGCaaaaaa < 1:2344290/35‑1 (MQ=255)
gTTTGCAGTACCGTTATGAGGGAAAGCAAAAAATGCTGGCACTTGGGGTTTATCCTGAAATCACACt < 1:1824102/67‑1 (MQ=255)
gTTTGCAGTACCGTTATGAGGGAAAGCAAAAAATGCTGGCACTTGGGGTTTATCCTGAAATCACACt < 1:3189260/67‑1 (MQ=255)
ttGCAGTACCGTTATGAGGGAAAGCAGAAAATGCTGGCACTTGGGGTTTATCCTGAAATCACACTAGCg < 1:2105824/69‑1 (MQ=255)
ttGCAGTACCGTTATGAGGGAAAGCAGAAAATGCTGGCACTTGGGGTTTATCCTGAAATCACACTAGCg < 1:3521004/69‑1 (MQ=255)
tGCAGTACCGTTATGAGGGAAAGCAGAAAATGCTGGCACTTGGGGTTTa < 1:1847121/49‑1 (MQ=255)
tGCAGTACCGTTATGAGGGAAAGCAGAAAATGCTGGCACTTGGGGTTTATCCTGAAATCACACTAGCgg > 1:2939010/1‑69 (MQ=255)
tGCAGTACCGTTATGAGGGAAAGCAGAAAATGCTGGCACTTGGGGTTTATCCTGAAATCACACTAGCg < 1:1831301/68‑1 (MQ=255)
tGCAGTACCGTTATGAGGGAAACCAGAAAATGCTGGCACTTGGGGTTTa < 1:467074/49‑1 (MQ=39)
ccGTTATGAGGGAAAGCAGAAAATGCTGGCACTTGGGGtt < 1:3468265/40‑1 (MQ=255)
ccGTTATGAGGGAAAGCAGAAAATGCTGGCACTTGGGGtt < 1:2639497/40‑1 (MQ=255)
ccGTTATGAGGGAAAGCAGAAAATGCTGGCACTTGGGGTTTATCCTGAAATCACACTAGCg > 1:2801363/1‑61 (MQ=255)
ccGTTATGAGGGAAAGCAGAAAATGCTGGCACTTGGGGTTTATCCTGAAATCACACTAGCg > 1:2283832/1‑61 (MQ=255)
ccGTTATGAGGAAAAGCAGAAAATGCTGGCACTTGGGGTTTATCCTGAAATCACACTAGAGGATGCCag > 1:802661/1‑69 (MQ=255)
aTGAGGGAAAGCAGAAAATGCTGGCACTTGTGGTTTATCCTGAAATCACACTAGCGGATGCCag < 1:3270027/64‑1 (MQ=255)
aaaGCAGAAAATGCTGGCACTTGGGGTTTATCCTGAAATCACACTAGCGGATGCCAGAGt > 1:3543800/1‑60 (MQ=255)
aaaGCAGAAAATGCTGGCACTTGGGGTTTATCCTGAAATCACACTAGCGGATGCCAGAGt > 1:576973/1‑60 (MQ=255)
aaaGCAGAAAATGCTGGCACTTGGGGTTTATCCTGAAATCACACTAGCGGATGCCAGAGt > 1:1428913/1‑60 (MQ=255)
aaaGCAGAAAATGCTGGCACTTGGGGTTTATCCTGAAATCACACTAGCGGATGCCAGAGt > 1:801805/1‑60 (MQ=255)
|
CATCTGCTTGTCCATCCAAATGGTTCTAAGTACTGGCGTTTGCAGTACCGTTATGAGGGAAAGCAAAAAATGCTGGCACTTGGGGTTTATCCTGAAATCACACTAGCGGATGCCAGAGT > W3110S.gb/4501435‑4501553
|
| 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
