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 R1
|
311 |
50.1 |
4085234 |
95.9% |
3917739 |
60.7 |
Breseq alignment
BRESEQ :: Evidence
|
| evidence |
seq id |
position |
mutation |
freq |
annotation |
gene |
description |
| RA |
W3110S.gb |
2,002,183 |
G→A |
36.8% |
R114C (CGC→TGC) |
fliY ← |
cystine transporter subunit |
|
| |
seq id |
position |
ref |
new |
freq |
score (cons/poly) |
reads |
annotation |
genes |
product |
| * | W3110S.gb | 2,002,183 | 0 | G | A | 36.8%
| 52.3
/ 58.0
| 57 | R114C (CGC→TGC) | fliY | cystine transporter subunit |
| Reads supporting (aligned to +/- strand): ref base G (23/13); new base A (15/6); total (38/19) |
| Fisher's exact test for biased strand distribution p-value = 7.72e-01 |
| Kolmogorov-Smirnov test that lower quality scores support variant p-value = 9.80e-01 |
ACCTTTTTTCACCAGCGCCTGAATACCAGAAATGGTGTACGGGGTTGAGAAATCGTA‑TTTTTTCTTGCGCTCATCAGAAATGGTGACCTGATTAATCACCACATCAATACGTTTAGAGTCCAGCGACGC > W3110S.gb/2002115‑2002243
|
aCCTTTTTTCACCAGCGCCTGAATACCAGAAATGGTGTACGGGGTTGAGAAATCGTA‑TTTTTTCTTGCGCt > 1:3088513/1‑71 (MQ=255)
aCCTTTTTTCACCAGCGCCTGAATACCAGAAATGGTGTACGGGGTTGAGAAATCGTA‑TTTTTTCTTGCGCt > 1:2071102/1‑71 (MQ=255)
ttttttGACCAGCGCCTGAATACCAGAAATGGTGTACGGGGTTGAGAAATCGTA‑TTTTTTCTTGCACtcat > 1:524010/1‑71 (MQ=255)
ttttttCACCAGCGCCTGAATACCAGAAATGGTGTACGGGGTTGAGAAATCGTA‑TTTTTTCTTGCACtcat > 1:1276152/1‑71 (MQ=255)
ttttCACCAGCGCCTGAATACCAGAAATGGTGTACGGGGTTGAGAAATCGTA‑TTTTTTCTTGCGCtcatc < 1:2580435/70‑1 (MQ=255)
ttttCACCAGCGCCTGAATACCAGAAATGGTGTACGGGGTTGAGAAATCGTA‑TTTTTTCTTGCGCtcat < 1:2547081/69‑1 (MQ=255)
ttttCACCAGCGCCTGAATACCAGAAATGGTGTACGGGGTTGAGAAATCGTA‑TTTTTTCTTGCGCtcat < 1:1345670/69‑1 (MQ=255)
ttttCACCAGCGCCTGAATACCAGAAATGGTGTACGGGGTTGAGAAATCGTA‑TTTTTTCTTGCGCtcat < 1:1462983/69‑1 (MQ=255)
ttCACCAGCGCCTGAATACCAGAAATGGTGTACGGGGTTGAGAAATCGTA‑TTTTTTCTTGCGCTCATCAg > 1:2680558/1‑70 (MQ=255)
tCACCAGCGCCTGAATACCAGAAATGGTGTACGGGGTTGAGAAATCGTA‑TTTTTTCTTGCGCTCATCAGa < 1:3539851/70‑1 (MQ=255)
cgcCTGAATACCAGAAATGGTGTACGGGGTTGAGAAATCGTA‑TTTTTTCTTGCGCTCATCAGAAATGGTGa < 1:338706/71‑1 (MQ=255)
gcCTGAATACCAGAAATGGTGTACGGGGTTGAGAAATCGTA‑TTTTTTCTTGCGCTCATCAGAAATGGTGAc > 1:1551138/1‑71 (MQ=255)
gcCTGAATACCAGAAATGGTGTACGGGGTTGAGAAATCGTA‑TTTTTTCTTGCGCTCATCAGAAATGGTGAc > 1:3296264/1‑71 (MQ=255)
cTGAATACCAGAAATGGTGTACGGGGTTGAGAAATCGTA‑TTTTTTCTTGCACTCATCAGAAATGGTGACCt > 1:3024189/1‑71 (MQ=255)
gAATACCAGAAATGGTGTACGGGGTTGAGAAATCGTA‑TTTTTTCTTGCACTCATCAGAAATGGTGACCTGa > 1:2548729/1‑71 (MQ=255)
aaTACCAGAAATGGTGTACGGGGTTGAGAAATCGTA‑TTTTTTCTTGCGCTCATCAGaaa > 1:3982026/1‑59 (MQ=255)
aaTACCAGAAATGGTGTACGGGGTTGAGAAATCGTA‑TTTTTTCTTGCGCTCATCAGaaa > 1:728134/1‑59 (MQ=255)
aTACCAGAAATGGTGTACGGGGTTGAGAAATCGTA‑TTTTTTCTTGCACTCATCAGAAATGGTGACCTGAtt < 1:2496888/71‑1 (MQ=255)
tACCAGAAATGGTGTACGGGGTTGAGAAATCGTA‑TTTTTTCTTGCGCTCATCAGAAATGGTGACCTGATTa < 1:3263912/71‑1 (MQ=255)
tACCAGAAATGGTGTACGGGGTTGAGAAATCGTA‑TTTTTTCTTGCGCTCATCAGAAATGGTGACCTGACTa < 1:1701119/71‑1 (MQ=255)
tACCAGAAATGGTGTACGGGGTTGAGAAATCGTA‑TTTTTTCTTGCACTCATCAGAAATg < 1:1775089/59‑1 (MQ=255)
ccAGAAATGGTGTACGGGGTTGAGAAATCGTA‑TTTTTTCTTGCGCTCATCAGAAATGGTGACCTGATTAAt > 1:3278402/1‑71 (MQ=255)
cAGAAATGGTGTACGGGGTTGAGAAATCGTATTTTTTTCTTGCGCTCATCAGAAATGGTGACCTGATTaa > 1:2260464/1‑70 (MQ=255)
aaaTGGTGTACGGGGTTGAGAAATCGTA‑TTTTTTCTTGCACTCATCAGAAATGGTGACCt < 1:35295/60‑1 (MQ=255)
aaTGGTGTACGGGGTTGAGAAATCGTA‑TTTTTTCTTGCGCTCATCAGAAATGGTGACCTGATTAATcacca > 1:1511546/1‑71 (MQ=255)
aaTGGTGTACGGGGTTGAGAAATCGTA‑TTTTTTCTTGCGCTCATCAGAAATGGTGACCTGATTAATcacca > 1:2122893/1‑71 (MQ=255)
aTGGTGTACGGGGTTGAGAAATCGTA‑TTTTTTCTTGCGCTCATCAGaaa > 1:3915374/1‑49 (MQ=255)
aTGGTGTACGGGGTTGAGAAATCGTA‑TTTTTTCTTGCACTCATCAGaaa > 1:1203845/1‑49 (MQ=255)
aTGGTGTACGGGGTTGAGAAATCGTA‑TTTTTTCTTGCACTCATCAGaaa > 1:1601421/1‑49 (MQ=255)
ggTGTACGGGGTTGAGAAATCGTA‑TTTTTTCTTGCGCTCATCAGAAAt < 1:2365650/48‑1 (MQ=255)
tgtACGGGGTTGAGAAATCGTA‑TTTTTTCTTGCGCTCATCAGAAATgg > 1:3184199/1‑48 (MQ=255)
tACGGGGTTGAGAAATCGTA‑TTTTTTCTTGCACTCATCAGAAATGGTGACCt < 1:2128684/52‑1 (MQ=255)
cGGGGTTGAGAAATCGTA‑TTTTTTCTTGCGCTCATCAGAAATGGTGACCTGATTAATcacca > 1:3772417/1‑62 (MQ=255)
cGGGGTTGAGAAATCGTA‑TTTTTTCTTGCGCTCATCAGAAATGGTGACCTGATTAATCACCACATCAATAc > 1:489107/1‑71 (MQ=255)
cGGGGTTGAGAAATCGTA‑TTTTTTCTTGCACTCATCAGAAATGGTGACCTGATTAATCACCACATCAATAc > 1:15075/1‑71 (MQ=255)
cGGGGTTGAGAAATCGTA‑TTTTTTCTTGCACTCATCAGAAATGGTGACCTGATTAATCACCACATCAATAc > 1:1328503/1‑71 (MQ=255)
gggTTGAGAAATCGTA‑TTTTTTCTTGCGCTCATCAGAAATGGTGACCTGATTAATCACCACATCAATACGt > 1:1246037/1‑71 (MQ=255)
ttGAGAAATCGTA‑TTTTTTCTTGCACTCATCAGAAATGGTGACCTGATTAATCACCACATCAATACGTTTa < 1:1393421/71‑1 (MQ=255)
gagaAATCGTA‑TTTTTTCTTGCACTCATCAGAAATGGTGACCTGATTAATCACCACATCAATACGTTTa > 1:2802373/1‑69 (MQ=255)
gagaAATCGTA‑TTTTTTCTTGCACTCATCAGAAATGGTGACCTGATTAATCACCACATCAATACGTTTa > 1:130498/1‑69 (MQ=255)
aaaTCGTA‑TTTTTTCTTGCGCTCATCAGAAATGGTGACCTGATTAATgacc > 1:2181041/1‑51 (MQ=255)
aaaTCGTA‑TTTTTTCTTGCGCTCATCAGAAATGGTGACCTGATTAATcacca > 1:553682/1‑52 (MQ=255)
aaaTCGTA‑TTTTTTCTTGCGCTCATCAGAAATGGTGACCTGATTAATcacca > 1:1303089/1‑52 (MQ=255)
tCGTA‑TTTTTTCTTGCACTCATCAGAAATGGTGACCTGATTAATCACCACATCAATACGTTTa < 1:1256549/63‑1 (MQ=255)
cGTA‑TTTTTTCTTGCACTCATCAGAAATGGTGACCTGATTa > 1:2273498/1‑41 (MQ=255)
cGTA‑TTTTTTCTTGCACTCATCAGAAATGGTGACCTGATTAAt > 1:594798/1‑43 (MQ=255)
cGTA‑TTTTTTCTTGCACTCATCAGAAATGGTGACCTGATTAAt > 1:2402516/1‑43 (MQ=255)
cGTA‑TTTTTTCTTGCACTCATCAGAAATGGTGACCTGATTAAt > 1:3970046/1‑43 (MQ=255)
gTA‑TTTTTTCTTGCGCTCATCAGAAATGGTGACCTGATTAATCACCACATCAATACGTTTAGAGTCCAGc > 1:3454300/1‑70 (MQ=255)
gTA‑TTTTTTCTTGCGCTCATCAGAAATGGTGACCTGATTAATCACCACATCAATACGTTTAGAGTCCAGc < 1:2886339/70‑1 (MQ=255)
gTA‑TTTTTTCTTGCGCTCATCAGAAATGGTGACCTGATTAATCACCACATCAATACGTTTAGAGTCCAGCg < 1:1574933/71‑1 (MQ=255)
gTA‑TTTTTTCTTGCACTCATCAGAAATGGTGACCTGATTAATCACCACATCAATACGTTTAGAGTCCAGc > 1:3860297/1‑70 (MQ=255)
a‑TTTTTTCTTGCGCTCATCAGAAATGGTGACCTGATTAATCACCACATCAATACGTTTagag < 1:1068186/62‑1 (MQ=255)
a‑TTTTTTCTTGCGCTCATCAGAAATGGTGACCTGATTAAT‑ACCACATCAATACGTTTagag < 1:1362837/61‑1 (MQ=255)
tttttCTTGCGCTCATCAGAAATGGTGACCTGATTAATCACCACATCAATACGTTTAGAGTc > 1:1305446/1‑62 (MQ=255)
ttttCTTGCGCTCATCAGAAATGGTGACCTGATTAATCACCACATCAATACGTTTAGAGTCCAGCGACGc > 1:3816196/1‑70 (MQ=255)
ttttCTTGCGCTCATCAGAAATGGTGACCTGATTAATCACCACATCAATACGTTTAGAGTCCAGCGACGc > 1:898766/1‑70 (MQ=255)
|
ACCTTTTTTCACCAGCGCCTGAATACCAGAAATGGTGTACGGGGTTGAGAAATCGTA‑TTTTTTCTTGCGCTCATCAGAAATGGTGACCTGATTAATCACCACATCAATACGTTTAGAGTCCAGCGACGC > W3110S.gb/2002115‑2002243
|
| 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
