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 F8 I0 R2
|
422 |
46.8 |
3726540 |
94.7% |
3529033 |
61.7 |
Breseq alignment
BRESEQ :: Evidence
|
| evidence |
seq id |
position |
mutation |
freq |
annotation |
gene |
description |
| RA |
W3110S.gb |
4,501,500 |
A→G |
100% |
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 | 87.8%
| 136.2
/ 9.5
| 49 | Q23Q (CAA→CAG) | intB | predicted integrase |
| Reads supporting (aligned to +/- strand): ref base A (5/1); new base G (27/16); total (32/17) |
| Fisher's exact test for biased strand distribution p-value = 6.50e-01 |
| Kolmogorov-Smirnov test that lower quality scores support variant p-value = 7.56e-01 |
| Rejected as polymorphism: Variant not supported by required number of reads on each strand. |
CATCTGCTTGTCCATCCAAATGGTTCTAAGTACTGGCGTTTGCAGTACCGTTATGAGGGAAAGCAAAAAATGCTGGCACTTGGGGTTTATCCTGAAATCACACTAGCGGATGCCAGAGTACGTCGTGAC > W3110S.gb/4501435‑4501563
|
cATCTGCTTGTCCATCCAAATGGTTCTAAGTACTGTCGTTTGCAGTACCGTTATGAGGGAAAGCAGAAAAt < 1:2593571/71‑1 (MQ=255)
cATCTGCTTGTCCATCCAAATGGTTCTAAGTACTGGCGTTTGCAGTACCGTTATGAGGGAAAGCAGAAAAt < 1:962973/71‑1 (MQ=255)
cATCTGCTTGTCCATCCAAATGGTTCTAAGTACTGGCGTTTGCAGTACCGTTATGAGGGAAAGCAGAAAAt < 1:2096695/71‑1 (MQ=255)
cATCTGCTTGTCCATCCAAATGGTTCTAAGTACTGGCGTTTGCAGTACCGTTATGAGGGAAAGCAGAAAAt < 1:2285995/71‑1 (MQ=255)
cATCTGCTTGTCCATCCAAATGGTTCTAAGTACTGGCGTTTGCAGTACCGTTATGAGGGAAAGCAGAAAAt < 1:388257/71‑1 (MQ=255)
tGCTTGTCCATCCAAATGGTTCTAAGTACTGGCGTTTGCAGTACCGTTATGAGGGAAAGCaaaaaa > 1:1590633/1‑66 (MQ=255)
catccaAATGGTTCTAAGTACTGGCGTTTGCAGTACCGTTATGAGGGAAAGCagaa > 1:339068/1‑56 (MQ=255)
catccaAATGGTTCTAAGTACTGGCGTTTGCAGTACCGTTATGAGGGAAAGCagaa > 1:2015971/1‑56 (MQ=255)
catccaAATGGTTCTAAGTACTGGCGTTTGCAGTACCGTTATGAGGGAAAGCagaa > 1:3552893/1‑56 (MQ=255)
catccaAATGGTTCTAAGTACTGGCGTTTGCAGTACCGTTATGAGGGAAAGCagaa > 1:1885180/1‑56 (MQ=255)
catccaAATGGTTCTAAGTACTGGCGTTTGCAGTACCGTTATGAGGGAAAGCagaa > 1:767966/1‑56 (MQ=255)
catccaAATGGTTCTAAGTACTGGCGTTTGCAGTACCGTTATGAGGGAAAGCagaa > 1:1701115/1‑56 (MQ=255)
catccaAATGGTTCTAAGTACTGGCGTTTGCAGTACCGTTATGAGGGAAAGCagaa > 1:922510/1‑56 (MQ=255)
tccaAATGGTTCTAAGTACTGGCGTTTGCAGTACCGTTATGAGGGAAAGCAAAAAATGCTGGCACTTgggg > 1:3225185/1‑71 (MQ=255)
tccaAATGGTTCTAAGTACTGGCGTTTGCAGTACCGTTATGAGGGAAAGCAAAAAATGCTGGCACTTgggg > 1:1437929/1‑71 (MQ=255)
tccaAATGGTTCTAAGTACTGGCGTTTGCAGTACCGTTATGAGGGAAAGCAAAAAATGCTGGCACTTgggg > 1:1364582/1‑71 (MQ=255)
caAATGGTTCTAAGTACTGGCGTTTGCAGTACCGTTATTAGGGAAAGCAGAAAATGCTGGCACTTGGGGtt < 1:835837/71‑1 (MQ=255)
caAATGGTTCTAAGTACTGGCGTTTGCAGTACCGTTATGAGGGAAAGCAGAAAATGCTGGCACTTGGGGtt > 1:3135387/1‑71 (MQ=255)
caAATGGTTCTAAGTACTGGCGTTTGCAGTACCGTTATGAGGGAAAGCAGAAAATGCTGGCACTTGGGGtt > 1:2450370/1‑71 (MQ=255)
caAATGGTTCTAAGTACTGGCGTTTGCAGTACCGTTATGAGGGAAAGCAGAAAATGCTGGCACTTGGGGtt > 1:2602027/1‑71 (MQ=255)
caAATGGTTCTAAGTACTGGCGTTTGCAGTACCGTTATGAGGGAAAGCAGAAAATGCTGGCACTTGGGGtt > 1:1069618/1‑71 (MQ=255)
aaTGGTTCTAAGTACTGGCGTTTGCAGTACCGTTATGAGGGAAAGCAGAAAATGc < 1:3355092/55‑1 (MQ=255)
aaTGGTTCTAAGTACTGGCGTTTGCAGTACCGTTATGAGGGAAAGCAGAAAATGc < 1:1888175/55‑1 (MQ=255)
aaTGGTTCTAAGTACTGGCGTTTGCAGTACCGTTATGAGGGAAAGCAGAAAATGc < 1:1337734/55‑1 (MQ=255)
tGGTTCTAAGTACTGGCGTTTGCAGTACCGTTATGAGGGAAAGCAGAAAATGCt > 1:1135006/1‑54 (MQ=255)
tGGTTCTAAGTACTGGCGTTTGCAGTACCGTTATGAGGGAAAGCAGAAAATGCTg > 1:2414306/1‑55 (MQ=255)
aGTACTGGCGTTTGCAGTACCGTTTTGAGGGAAAGCAGAAAATGCTGGCACTTGGGGTTTATCCTGAAAt > 1:1996724/1‑70 (MQ=255)
aGTACTGGCGTTTGCAGTACCGTTATGAGGGAAAGCAGAAAATGCTGGCACTTGGGGTTTATCCTGAAAt > 1:976184/1‑70 (MQ=255)
aCTGGCGTTTGCAGTACCGTTATGAGGGAAAGCAGAAAAt > 1:2267109/1‑40 (MQ=255)
aCTGGCGTTTGCAGTACCGTTATGAGGGAAAGCAGAAAATGCTGGCACTTGGGGTTTATCCTGAAAt > 1:113248/1‑67 (MQ=255)
aCTGGCGTTTGCAGTACCGTTATGAGGGAAAGCAAAAAATGCTGGCACTTGGGGTTTATCCTGAAATcaca > 1:2397190/1‑71 (MQ=255)
tGCAGTACCGTTATGAGGGAAAGCAGAAAATGCTGGCACTTGGGGTTTATCCTGAAATCACACTAGCGGAt > 1:2370183/1‑71 (MQ=255)
tGCAGTACCGTTATGAGGGAAAGCAGAAAATGCTGGCACTTGGGGTTTATCCTGAAATCACACTAGCGGAt > 1:3542168/1‑71 (MQ=255)
gTACCGTTATGAGGGAAAGCAGAAAATGCTGGCACTTGGGGTTTATCCTGAAATCacac < 1:3586218/59‑1 (MQ=255)
aCCGTTATGAGGGAAAGCAGAAAATGCTGGCACTTGGGGTTTATCCTGAAATCACACTAGCGGATGCCa > 1:3577057/1‑69 (MQ=255)
ccGTTATGAGGGAAAGCAGAAAATGCTGGCACTTGGGGTTTATCCTGaaa > 1:1907401/1‑50 (MQ=255)
ccGTTATGAGGGAAAGCAGAAAATGCTGGCACTTGGGGTTTATCCTGAAAt > 1:40686/1‑51 (MQ=255)
ccGTTATGAGGGAAAGCAGAAAATGCTGGCACTTGGGGTTTATCCTGAAAt > 1:3131418/1‑51 (MQ=255)
ccGTTATGAGGGAAAGCAGAAAATGCTGGCACTTGGGGTTTATCCTGAAAt > 1:892244/1‑51 (MQ=255)
ccGTTATGAGGGAAAGCAGAAAATGCTGGCACTTGGGGTTTATCCTGAAATCACACt > 1:2807995/1‑57 (MQ=255)
ccGTTATGAGGGAAAGCAGAAAATGCTGGCACTTGGGGTTTATCCTGAAATCACACTAGCGGATGCCagag > 1:1830661/1‑71 (MQ=255)
ccGTTATGAGGGAAAGCAGAAAATGCTGGCACTTGGGGTTTATCCTGAAATCACACTAGCGGATGCCagag > 1:723671/1‑71 (MQ=255)
ccGTTATGAGGGAAAGCAAAAAATGCTGGCACTTGGGGTTTATCCTGAAATCACACTAGCGGATGCCagag > 1:863218/1‑71 (MQ=255)
gTTATGAGGGAAAGCAGAAAATGCTGGCACTTGGGGTTTATCCTGAAATCACACTAGCGGATGCCAGAGTa > 1:64276/1‑71 (MQ=255)
gTTATGAGGGAAAGCAGAAAATGCTGGCACTTGGGGTTTATCCTGAAATCACACTAGCGGATGCCAGAGTa > 1:3711212/1‑71 (MQ=255)
gTTATGAGGGAAAGCAGAAAATGCTGGCACTTGGGGTTTATCCTGAAATCACACTAGCGGATGCCAGAGTa > 1:1049400/1‑71 (MQ=255)
gTTATGAGGGAAAGCAGAAAATGCTGGCACTTGGGGTTTATCCTGAAATCACACTAGCGGATGCCAGAGTa > 1:2821603/1‑71 (MQ=255)
aTGAGGGAAAGCAGAAAATGCTGGCACTTGGGGTTTATCCTGAAATCACACTAGCGGATGCCAGAGTAcgt > 1:3503535/1‑71 (MQ=255)
aTGAGGGAAAGCAGAAAATGCTGGCACTTGGGGTTTATCCTGAAATCACACTAGCGGATGCCAGAGTAcgt > 1:2380507/1‑71 (MQ=255)
aTGAGGGAAAGCAGAAAATGCTGGCACTTGGGGTTTATCCTGAAATCACACTAGCGGATGCCAGAGTAcgt > 1:1643115/1‑71 (MQ=255)
tGAGGGAAAGCAGAAAATGCTGGCACTTGGGGTTTATCCTGa < 1:42973/42‑1 (MQ=255)
tGAGGGAAAGCAGAAAATGCTGGCACTTGGGGTTTATCCTGa < 1:362164/42‑1 (MQ=255)
tGAGGGAAAGCAGAAAATGCTGGCACTTGGGGTTTATCCTGa < 1:2900201/42‑1 (MQ=255)
tGAGGGAAAGCAGAAAATGCTGGCACTTGGGGTTTATCCTGAAATCACACTAGCGGATGCCAGAGTAcgt < 1:1863174/70‑1 (MQ=255)
aGGGAAAGCAAAAAATGCTGGCACTTGGGGTTTATCCTGAAATCACACTAGCGGATGCCAGAGTAcgtcgt < 1:506451/71‑1 (MQ=255)
aaaGCAGAAAATGCTGGCACTTGGGGTTTATCCTGAAATCACACTAGCGGATGCCAGAGTACGTCGTGAc < 1:2012395/70‑1 (MQ=255)
aaGCAGAAAATGCTGGCACTTGGGGTTTATCCTGAAATCACACTAGCGGATGCCAGAGTAcgtcgt < 1:592151/66‑1 (MQ=255)
|
CATCTGCTTGTCCATCCAAATGGTTCTAAGTACTGGCGTTTGCAGTACCGTTATGAGGGAAAGCAAAAAATGCTGGCACTTGGGGTTTATCCTGAAATCACACTAGCGGATGCCAGAGTACGTCGTGAC > W3110S.gb/4501435‑4501563
|
| Alignment Legend |
|---|
Aligned base mismatch/match (shaded by quality score): ATCG/ATCG < 3 ≤ ATCG/ATCG < 14 ≤ ATCG/ATCG < 32 ≤ ATCG/ATCG < 36 ≤ ATCG/ATCG |
Unaligned base: atcg Masked matching base: atcg Alignment gap: ‑ Deleted base: ‑ |
GATK/CNVnator alignment
N/A
