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 |
|
A2 F1 I0 R1
|
4577 |
57.4 |
3436498 |
77.7% |
2670158 |
63.4 |
Breseq alignment
BRESEQ :: Evidence
|
| evidence |
seq id |
position |
mutation |
freq |
annotation |
gene |
description |
| RA |
minE |
2,443,474 |
A→T |
49.1% |
R554R (CGT→CGA) |
ilvD ← |
dihydroxyacid dehydratase |
|
| |
seq id |
position |
ref |
new |
freq |
score (cons/poly) |
reads |
annotation |
genes |
product |
| * | minE | 2,443,474 | 0 | A | T | 49.1%
| ‑4.5
/ 66.7
| 55 | R554R (CGT→CGA) | ilvD | dihydroxyacid dehydratase |
| Reads supporting (aligned to +/- strand): ref base A (14/14); new base T (12/15); total (26/29) |
| Fisher's exact test for biased strand distribution p-value = 7.89e-01 |
| Kolmogorov-Smirnov test that lower quality scores support variant p-value = 7.41e-01 |
ACCTCGAGCGTCCTGCGCTTCACGACGCGCCGCCAGTTCGGCATCGCTTACCTGTAACTGAATGCCACGGTTCGGGATGTCGATAGCGATCAGGTCACCATCTTCAATCAGGCCAATGCTGCCGC > minE/2443408‑2443532
|
aCCTCGAGCGTCCTGCGCTTCACGATGCGCCGCCAGTTCGGCATCGCTTACCTGTAACTGAATGCCACg > 1:2802255/1‑69 (MQ=255)
aCCTCGAGCGTCCTGCGCTTCACGACGCGCCGCCAGTTCGGCATCGCTTACCTGTAACTGAATGCCACg > 1:2491402/1‑69 (MQ=255)
gCGTCCTGCGCTTCACGACGCGCCGCCAATTCGGCATCGCTTACCTGTAACTGAATGCCACGGTTCggg < 1:39871/69‑1 (MQ=255)
gCGTCCTGCGCTTCACGACGCGCCGCCAATTCGGCATCGCTTACCTGTAACTGAATGCCACGGTTCggg < 1:2228603/69‑1 (MQ=255)
cGTCCTGCGCTTCACGACGCGCCGCCAATTCGGCATCGCTTACCTGTAACTGAATGCCACGGTTCggg < 1:1292193/68‑1 (MQ=255)
tacTGCGCTTCACGACGCGCCGCCAGTTCGGCATCGCTTACCTGTAACTGAATGCCACGGTTCGGGATg > 1:1681278/3‑69 (MQ=255)
tCCTGCGCTTCACGACGCGCCGCCAGTTCGGCATCGCTTACCTGTAACTGAATGCCACGGTTCGGGATg > 1:1088104/1‑69 (MQ=255)
tCCTGCGCTTCACGACGCGCCGCCAGTTCGGCATCGCTTACCTGTAACTGAATGCCACGGTTCGGGATg > 1:1092173/1‑69 (MQ=255)
tCCTGCGCTTCACGACGCGCCGCCAGTTCGGCATCGCTTACCTGTAACTGAATGCCACGGTTCGGGATg > 1:774055/1‑69 (MQ=255)
tCCTGCGCTTCACGACGCGCCGCCAGTTCGGCATCGCTTACCTGTAACTGAATGCCACGGTTCGGGATg > 1:3107954/1‑69 (MQ=255)
tCCTGCGCTTCACGACGCGCCGCCAGTTCGGCATCGCTTACCTGTAACTGAATGCCACGGTTCGGGATg > 1:305395/1‑69 (MQ=255)
tCCTGCGCTTCACGACGCGCCGCCAGTTCGGCATCGCTTACCTGTAACTGAATGCCACGGTTCGGGATg > 1:2665052/1‑69 (MQ=255)
tCCTGCGCTTCACGACGCGCCGCCAGTTCGGCATCGCTTACCTGTAACTGAATGCCACGGTTCGGGATg > 1:1443282/1‑69 (MQ=255)
cTGCGCTTCACGACGCGCCGCCAGTTCGGCATCGCTTACCTGTAACTGAATGCCACGGTTCGGGATGTc < 1:2403256/69‑1 (MQ=255)
cTGCGCTTCACGACGCGCCGCCAGTTCGGCATCGCTTACCTGTAACTGAATGCCACGGTTCGGGATGTc < 1:1214242/69‑1 (MQ=255)
acgCGCCGCCAGTTCGGCATCGCTTACCTGTAACTGAATGCCACGGTTCGGGATGTCGATAGCGATCAg < 1:12803/69‑1 (MQ=255)
acgCGCCGCCAGTTCGGCATCGCTTACCTGTAACTGAATGCCACGGTTCGGGATGTCGATAGCGATCAg < 1:1587216/69‑1 (MQ=255)
acgCGCCGCCAGTTCGGCATCGCTTACCTGTAACTGAATGCCACGGTTCGGGATGTCGATAGCGATCAg < 1:856003/69‑1 (MQ=255)
acgCGCCGCCAGTTCGGCATCGCTTACCTGTAACTGAATGCCACGGTTCGGGATGTCGATAGCGATCAg < 1:724254/69‑1 (MQ=255)
acgCGCCGCCAGTTCGGCATCGCTTACCTGTAACTGAATGCCACGGTTCGGGATGTCGATAGCGATCAg < 1:1488539/69‑1 (MQ=255)
acgCGCCGCCAGTTCGGCATCGCTTACCTGTAACTGAATGCCACGGTTCGGGATGTCGATAGCGATCAg < 1:2353894/69‑1 (MQ=255)
acgCGCCGCCAGTTCGGCATCGCTTACCTGTAACTGAATGCCACGGTTCGGGATGTCGATAGCGATCAg < 1:2616869/69‑1 (MQ=255)
acgCGCCGCCAGTTCGGCATCGCTTACCTGTAACTGAATGCCACGGTTCGGGATGTCGATAGCGATCAg < 1:631384/69‑1 (MQ=255)
ccgccAGTTCGGCATCGCTTACCTGTAACTTAATGCCTCGGTTCGGAATATCGa < 1:362412/54‑1 (MQ=255)
ccgccAGTTCGGCATCGCTTACCTGTAACTGAATGCCTCGGTTCGGAATATCGa < 1:2410952/54‑1 (MQ=255)
ccgccAGTTCGGCATCGCTTACCTGTAACTGAATGCCTCGGTTCGGAATATCGa < 1:1179591/54‑1 (MQ=255)
ccgccAGTTCGGCATCGCTTACCTGTAACTGAATGCCTCGGTTCGGAATATCGa < 1:2894550/54‑1 (MQ=255)
ccgccAGTTCGGCATCGCTTACCTGTAACTGAATGCCTCGGTTCGGAATATCGa < 1:2738976/54‑1 (MQ=255)
ccgccAGTTCGGCATCGCTTACCTGTAACTGAATGCCTCGGTTCGGAATATCGa < 1:444831/54‑1 (MQ=255)
ccgccAGTTCGGCATCGCTTACCTGTAACTGAATGCCTCGGTTCGGAATATCGa < 1:2661596/54‑1 (MQ=255)
ccgccAGTTCGGCATCGCTTACCTGTAACTGAATGCCTCGGTTCGGAATATCGa < 1:683089/54‑1 (MQ=255)
ccgccAGTTCGGCATCGCTTACCTGTAACTGAATGCCTCGGTTCGGAATATCGa < 1:713795/54‑1 (MQ=255)
ccgccAGTTCGGCATCGCTTACCTGTAACTGAATGCCTCGGTTCGGAATATCGa < 1:2228461/54‑1 (MQ=255)
ccgccAGTTCGGCATCGCTTACCTGTAACTGAATGCCTCGGTTCGGAATATCGa < 1:2224484/54‑1 (MQ=255)
ccgccAGTTCGGCATCGCTTACCTGTAACTGAATGCCTCGGTTCGGAATATCGa < 1:2104360/54‑1 (MQ=255)
ccgccAGTTCGGCATCGCTTACCTGTAACTGAATGCCTCGGTTCGGAATATCGa < 1:169455/54‑1 (MQ=255)
ccgccAGTTCGGCATCGCTTACCTGTAACTGAATGCCTCGGTTCGGAATATCGa < 1:1541594/54‑1 (MQ=255)
ccgccAGTTCGGCATCGCTTACCTGTAACTGAATGCCTCGGTTCGGAATATCGa < 1:161710/54‑1 (MQ=255)
tCGCTTACCTGTAACTGAATGCCACGGTTCGGGATGTCGATAGCGATCAGGTCACCATc > 1:313068/1‑59 (MQ=255)
gCTTACCTGTAACTGAATGCCACGGTTCGGGATGTCGATAGCGATCAGGTCCCCATCTTCAATCAGGcc > 1:1588842/1‑69 (MQ=255)
gTAACTGAATGCCTCGGTTCGGAATATCGATAGCGATCAGGTCACCATCTTCAATCAGGCCAAtgctgc > 1:973794/1‑69 (MQ=255)
gTAACTGAATGCCTCGGTTCGGAATATCGATAGCGATCAGGTCACCATCTTCAATCAGGCCAAtgctgc > 1:1171272/1‑69 (MQ=255)
gTAACTGAATGCCTCGGTTCGGAATATCGATAGCGATCAGGTCACCATCTTCAATCAGGCCAAtgctgc > 1:3383455/1‑69 (MQ=255)
gTAACTGAATGCCTCGGTTCGGAATATCGATAGCGATCAGGTCACCATCTTCAATCAGGCCAAtgctgc > 1:2978062/1‑69 (MQ=255)
gTAACTGAATGCCTCGGTTCGGAATATCGATAGCGATCAGGTCACCATCTTCAATCAGGCCAAtgctgc > 1:2807249/1‑69 (MQ=255)
gTAACTGAATGCCTCGGTTCGGAATATCGATAGCGATCAGGTCACCATCTTCAATCAGGCCAAtgctgc > 1:2693578/1‑69 (MQ=255)
gTAACTGAATGCCTCGGTTCGGAATATCGATAGCGATCAGGTCACCATCTTCAATCAGGCCAAtgctgc > 1:1283211/1‑69 (MQ=255)
gTAACTGAATGCCTCGGTTCGGAATATCGATAGCGATCAGGTCACCATCTTCAATCAGGCCAAtgctgc > 1:1329485/1‑69 (MQ=255)
gTAACTGAATGCCTCGGTTCGGAATATCGATAGCGATCAGGTCACCATCTTCAATCAGGCCAAtgctgc > 1:2484203/1‑69 (MQ=255)
gTAACTGAATGCCTCGGTTCGGAATATCGATAGCGATCAGGTCACCATCTTCAATCAGGCCAAtgctgc > 1:1911051/1‑69 (MQ=255)
gTAACTGAATGCCTCGGTTCGGAATATCGATAGCGATCAGGTCACCATCTTCAATCAGGCCAAtgctg > 1:2663565/1‑68 (MQ=255)
gTAACTCAATGCCTCGGTTCGGAATATCGATAGCGATCAGGTCACCATCTTCAATCAGACCAAtgctgc > 1:2197495/1‑69 (MQ=255)
aCTGAATGCCACGGTTCGGGATGTCGATAGCGATCAGGTCACCATCTTCAATCAGGcc > 1:2072258/1‑58 (MQ=255)
aCTGAATGCCACGGTTCGGGATGTCGATAGCGATCAGGTCACCATCTTCAATCAGGCCAATGCTgccgc > 1:100129/1‑69 (MQ=255)
tGAATGCCACGGTTCGGGATGTCGATAGCGATCAg < 1:1163533/35‑1 (MQ=255)
|
ACCTCGAGCGTCCTGCGCTTCACGACGCGCCGCCAGTTCGGCATCGCTTACCTGTAACTGAATGCCACGGTTCGGGATGTCGATAGCGATCAGGTCACCATCTTCAATCAGGCCAATGCTGCCGC > minE/2443408‑2443532
|
| 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
