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 |
1,927,287 |
T→C |
78.0% |
L45P (CTT→CCT) |
yobB → |
conserved hypothetical protein |
|
| |
seq id |
position |
ref |
new |
freq |
score (cons/poly) |
reads |
annotation |
genes |
product |
| * | W3110S.gb | 1,927,287 | 0 | T | C | 78.0%
| 60.2
/ 13.1
| 32 | L45P (CTT→CCT) | yobB | conserved hypothetical protein |
| Reads supporting (aligned to +/- strand): ref base T (4/3); new base C (7/17); total (12/20) |
| Fisher's exact test for biased strand distribution p-value = 2.10e-01 |
| Kolmogorov-Smirnov test that lower quality scores support variant p-value = 1.00e+00 |
CATCATCTGGAGTTTGTGAGGGCCGCCGCCAGGCAACAATGTCAGCTGTTAGTTTTTCCATCGCTTTCTTTACTGGGGTGTGATTATTCGCGACGTGCCCTTCCTGCCCCACCCGATCTCTCACT > W3110S.gb/1927223‑1927347
|
catcatCTGGAGTTTGTGAGGGCCGCCGCCAGGCAACAATGTCAGCTGTTAGTTTTTCCATCGccttct < 1:2645623/69‑1 (MQ=255)
catcatCTGGAGTTTGTGAGGGCCGCCGCCAGGCAACAATGTCAGCTGTTAGTTTTTCCATCGccttc > 1:2554778/1‑68 (MQ=255)
catcTGGAGTTTGTGAGGGCCGCCGCCAGGCAACAATGTCAGCTGTTAGTTTTTCCATCGctttcttt > 1:2409684/1‑68 (MQ=255)
catcTGGAGTTTGTGAGGGCCGCCGCCAGGCAACAATGTCAGCTGTTAGTTTTTCCATCGctttctt < 1:3234519/67‑1 (MQ=255)
catcTGGAGTTTGTGAGGGCCGCCGCCAGGCAACAATGTCAGCTGTTAGTTTTTCCATCGccttctt < 1:2637122/67‑1 (MQ=255)
catcTGGAGTTTGTGAGGGCCGCCGCCAGGCAACAATGTCAGCTGTTAGTTTTTCCATCGccttctt < 1:2568308/67‑1 (MQ=255)
catcTGGAGTTTGTGAGGGCCGCCGCCAGGCAACAATGTCAGCTGTTAGTTTTTCCATCGccttctt < 1:949160/67‑1 (MQ=255)
catcTGGAGTTTGTGAGGGCCGCCGCCAGGCAACAATGTCAGCTGTTAGTTTTTCCATCGccttctt < 1:2064218/67‑1 (MQ=255)
catcTGGAGTTTGTGAGGGCCGCCGCCAGGCAACAATGTCAGCTGTTAGTTTTTCCATCGacttctt < 1:656741/67‑1 (MQ=255)
catcTGGAGTTTGTGAGGGCCGCCGCCAGGCAACAATGTCAGCTGTTAGTTTTTCCATCGCTTTCTTTa < 1:1491234/69‑1 (MQ=255)
atcTGGAGTTTGTGATGGCCGCCGCCAGGCAACAATGTCAGCTGTTAGTTTTTCCATCGccttcttt < 1:1289772/67‑1 (MQ=255)
atcTGGAGTTTGTGAGGGCCGCCGCCAGGCAACAATGTCAGCTGTTAGTTTTTCCATCGccttcttt < 1:1150027/67‑1 (MQ=255)
tcTGGAGTTTGTGAGGGCCGCCGCCAGGCAACAATGTCAGCTGTTAGTTTTTCCATCGccttctt < 1:586564/65‑1 (MQ=255)
ttGTGAGGGCCGCCGCCAGGCAACAATGTCAGCTGTTAGTTTTTCCATCGCCTTCTTTACTGGGGtgtg < 1:2282139/69‑1 (MQ=255)
tgtgAGGGCCGCCGCCAGGCAACAATGTCAGCTGTTAGTTTTTCCATCGctttcttt < 1:441239/57‑1 (MQ=255)
tgtgAGGGCCGCCGCCAGGCAACAATGTCAGCTGTTAGTTTTTCCATCGctttcttt < 1:2160040/57‑1 (MQ=255)
tgtgAGGGCCGCCGCCAGGCAACAATGTCAGCTGTTAGTTTTTCCATCGctttcttt < 1:286728/57‑1 (MQ=255)
tgtgAGGGCCGCCGCCAGGCAACAATGTCAGCTGTTAGTTTTTCCATCGctttcttt < 1:2401232/57‑1 (MQ=255)
tgtgAGGGCCGCCGCCAGGCAACAATGTCAGCTGTTAGTTTTTCCATCGctttcttt < 1:251772/57‑1 (MQ=255)
tgtgAGGGCCGCCGCCAGGCAACAATGTCAGCTGTTAGTTTTTCCATCGctttcttt < 1:1285206/57‑1 (MQ=255)
tgtgAGGGCCGCCGCCAGGCAACAATGTCAGCTGTTAGTTTTTCCATCGCCTTCTTTACTGGGGtgtg > 1:2943944/1‑68 (MQ=255)
tgtgAGGGCCGCCGCCAGGCAACAATGTCAGCTGTTAGTTTTTCCATCGCCTTCTTTACTGGGGtgtg > 1:2998308/1‑68 (MQ=255)
tgAGGGCCGCCGCCAGGCAACAATGTCAGCTGTTAGTTTTTCCATCGCCTTCTTTACTGGGGTGTGat < 1:3401351/68‑1 (MQ=255)
tgAGGGCCGCCGCCAGGCAACAATGTCAGCTGTTAGTTTTTCCATCGCCTTCTTTACTGGGGTGTGat < 1:2570479/68‑1 (MQ=255)
ggCCGCCGCCAGGCAACAATGTCAGCTGTTAGTTTTTCCATCGCCTTCTTTACTGGGGTGTGattatt < 1:1890633/68‑1 (MQ=255)
ggCCGCCGCCAGGCAACAATGTCAGCTGTTAGTTTTTCCATCGCCTTCTTTACTGGGGTGTGattatt < 1:3518084/68‑1 (MQ=255)
gccgccgccAGGCAACAATGTCAGCTGTTAGTTTTTCCATCGccttcttt > 1:1386492/1‑50 (MQ=255)
ccAGGCAACAATGTCAGCTGTTAGTTTTTCCATCGCCTTCTTTACTGGGGTGTGATTATTCGCGACGTg < 1:403374/69‑1 (MQ=255)
gCAACAATGTCAGCTGTTAGTTTTTCCATCGCCTTCTTTACTGGGGTGTGat < 1:3588226/52‑1 (MQ=255)
gCAACAATGTAAGCTGTTAGTTTTTCCATCGCTTTCTTTACTGGGGTGTGATTATTCGCGACGTGCCCt < 1:76913/69‑1 (MQ=255)
aacaaTGTCAGCTGTTAGTTTTTCCATCGccttctt < 1:1292211/36‑1 (MQ=255)
aacaaTGTCAGCTGTTAGTTTTTCCATCGCCTTCTTTACTGGGgtgt < 1:1308364/47‑1 (MQ=255)
aaTGTCAGCTGTTAGTTTTTCCATCGCCTTCTTTACTGGGGTGTGattat < 1:315636/50‑1 (MQ=255)
aaTGTCAGCTGTTAGTTTTTCCATCGCCTTCTTTACTGGGGTGTGATTATTCGCGACGTGc > 1:984410/1‑61 (MQ=255)
aaTGTCAGCTGTTAGTTTTTCCATCGCCTTCTTTACTGGGGTGTGATTATTCGCGACGTGc > 1:1785483/1‑61 (MQ=255)
aTGTCAGCTGTTAGTTTTTCCATCGCCTTCTTTACTGGGGTGTGATTATTcgcg > 1:396326/1‑54 (MQ=255)
aTGTCAGCTGTTAGTTTTTCCATCGCATTCTTTACTGGGGTGTGATTATTcgcg > 1:1514420/1‑54 (MQ=255)
cAGCTGTTAGTTTTTCCATCGCTTTCTTTACTGGGGTGTGATTATTCGCGACg > 1:2172402/1‑53 (MQ=255)
cAGCTGTTAGTTTTTCCATCGCTTTCTTTACTGGGGTGTGATTATTCGCGACGTg > 1:2173075/1‑55 (MQ=255)
cAGCTGTTAGTTTTTCCATCGCTTTCTTTACTGGGGTGTGATTATTCGCGACGTg > 1:528297/1‑55 (MQ=255)
gTTAGTTTTTCCATCGCTTTCTTTACTGGGGTGTGATTATTCGCGACGTGCCCTTCCTGCCCCACCCGa > 1:3266178/1‑69 (MQ=255)
tAGTTTTTCCATCGCCTTCTTTACTGGGGTGTGATTATTCGCGACGTGCCCTTCCTGCCCCACCCGAtc > 1:2246874/1‑69 (MQ=255)
gTTTTTCCATCGCCTTCTTTACTGGGGTGTGATTATTCGCGACGTGCCCt < 1:3162588/50‑1 (MQ=255)
gTTTTTCCATCGCCTTCTTTACTGGGGTGTGATTATTCGCGACGTGCCCt < 1:556125/50‑1 (MQ=255)
tttCCATCGCCTTCTTTACTGGGGTGTGATTATTCGCGACGTGCCCTTCCTGCCCCACCCGATCTCTCa > 1:1391705/1‑69 (MQ=255)
tCCATCGCTTTCTTTACTGGGGTGTGATTATTCGCGACGTGCCCTTCCTGCCCCACCCGATCTCTCAc < 1:1217016/68‑1 (MQ=255)
tCCATCGCCTTCTTTACTGGGGTGTGATTATTCGCGACGTGCCCt < 1:1868428/45‑1 (MQ=255)
tCCATCGCCTTCTTTACTGGGGTGTGATTATTCGCGACGTGCCCt < 1:1735172/45‑1 (MQ=255)
tCCATCGCCTTCTTTACTGGGGTGTGATTATTCGCGACGTGCCCt < 1:1510943/45‑1 (MQ=255)
tCCATCGCCTTCTTTACTGGGGTGTGATTATTCGCGACCTGCCCt < 1:473980/45‑1 (MQ=255)
ccATCGCCTTCTTTACTGGGGTGTGATTATTCGCGACGTGCCCTTCCTGCCCCACCCGATCTCTCACt < 1:2565896/68‑1 (MQ=255)
ccATCGCCTTCTTTACTGGGGTGTGATTATTCGCGACGTGCCCTTCCTGCCCCACCCGATCTCTCACt < 1:3101030/68‑1 (MQ=255)
|
CATCATCTGGAGTTTGTGAGGGCCGCCGCCAGGCAACAATGTCAGCTGTTAGTTTTTCCATCGCTTTCTTTACTGGGGTGTGATTATTCGCGACGTGCCCTTCCTGCCCCACCCGATCTCTCACT > W3110S.gb/1927223‑1927347
|
| 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
