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 |
|
A5 F21 I0 R2
|
316 |
65.6 |
5147759 |
97.4% |
5013917 |
60.3 |
Breseq alignment
BRESEQ :: Evidence
|
| evidence |
seq id |
position |
mutation |
freq |
annotation |
gene |
description |
| RA |
W3110S.gb |
1,352,881 |
T→C |
34.8% |
intergenic (‑128/+240) |
fabI ← / ← ycjD |
enoyl‑[acyl‑carrier‑protein] reductase, NADH‑dependent/conserved hypothetical protein |
|
| |
seq id |
position |
ref |
new |
freq |
score (cons/poly) |
reads |
annotation |
genes |
product |
| * | W3110S.gb | 1,352,881 | 0 | T | C | 34.8%
| 18.4
/ 19.3
| 23 | intergenic (‑128/+240) | fabI/ycjD | enoyl‑[acyl‑carrier‑protein] reductase, NADH‑dependent/conserved hypothetical protein |
| Reads supporting (aligned to +/- strand): ref base T (8/7); new base C (4/4); total (12/11) |
| Fisher's exact test for biased strand distribution p-value = 1.00e+00 |
| Kolmogorov-Smirnov test that lower quality scores support variant p-value = 9.55e-01 |
GTAAACAGTACGAACAGATAAACGGTTATTATAATCAACCTGGCTGTGAGTAGCTATAGTTGCCAGGTCCGACCGGAGCAGGCTGCGGCAGGGGGGGCGCTTTTCCCCTCACCCTAACCCTCTCCCCAGAGG > W3110S.gb/1352814‑1352945
|
gTAAACAGTACGAACAGATAAACTGTTATTATAATCAACCTGGCTGTGAGTAGCTATAGTTGCCAGGCCCg < 1:4658997/71‑1 (MQ=255)
aaCAGTACGAACAGATAAACGGTTATTATAATCAACCTGGCTGTGAGTAGCTATAGTTGCCAGGTCCGAc > 1:230141/1‑70 (MQ=255)
aaCAGTACGAACAGATAAACGGTTATTATAATCAACCTGGCTGTGAGTAGCTATAGTTGCCAGGCCCGAcc > 1:4227480/1‑71 (MQ=255)
cAGTACGAACAGATAAACGGTTATTATAATCAACCTGGCTGTGAGTAGCTATAGTTGCCAGGCCCGACCgg < 1:46630/71‑1 (MQ=255)
agaaCGAACAGATAAACGGTTATTATAATCAAACTCGCTGTGAGTAGCTATAGTTGCCAGGTCCGa > 1:2764128/4‑66 (MQ=255)
aCGAACAGATAAACGGTTATTATAATCAACCTGGCTGTGAGTAGCTATAGTTGCCAGGTCCGACCg < 1:3954399/66‑1 (MQ=255)
aCGAACAGATAAACGGTTATTATAATCAACCTGGCTGTGAGTAGCTATAGTTGCCAGGTCCGACCGGAg > 1:1091770/1‑69 (MQ=255)
cGAACAGATAAACGGTTATTATAATCAACCTGGCTGTGAGTAGCTATAGTTGCCAGGCCCGACCGGAGCAg > 1:4815206/1‑71 (MQ=255)
gAACAGATAAACGGTTATTATAATCAACCTGGCTGTGAGTAGCTATAGTTGCCAGGTCCGACCGGAGCa < 1:2295641/69‑1 (MQ=255)
tAAACGGTTATTATAATCAACCTGGCTGTGAGTAGCTATAGTTGCCAGGCCCGACCGGAGCAGGCTGc > 1:2614607/1‑68 (MQ=255)
aaCGGTTATTATAATCAACCTGGCTGTGAGTAGCTATAGTTGCCAGGTCCGACCGGAGCAGGCTGCgg < 1:550167/68‑1 (MQ=255)
cGGTTATTATAATCAACCTGGCTGTGAGTAGCTATAGTTGCCAGGTCCGACCGGAGCAGGCTGCGGCa > 1:381436/1‑68 (MQ=255)
ggTTATTATAATCAACCTGGCTGTGAGTAGCTATAGTTGCCAGGCCCg < 1:4659917/48‑1 (MQ=255)
ttatAATCAACCTGGCTGTGAGTAGCTATAGTTGCCAGGTCCGACCg > 1:1873216/1‑47 (MQ=255)
ttatAATCAACCTGGCTGTGAGTAGCTATAGTTGCCAGGTCCGACCg > 1:2612090/1‑47 (MQ=255)
taATCAACCTGGCTGTGAGTAGCTATAGTTGCCAGGTCCGACCGGAGc > 1:708069/1‑48 (MQ=255)
taATCAACCTGGCTGTGAGTAGCTATAGTTGCCAGGTCCGACCGGAGc > 1:3724015/1‑48 (MQ=255)
taATCAACCTGGCTGTGAGTAGCTATAGTTGCCAGGTCCGACCGGAGCAGGCTGCGGCAGGGGGGGCGCtt < 1:4723143/71‑1 (MQ=255)
taATCAACCTGGCTGTGAGTAGCTATAGTTGCCAGGCCCGACCGGAGCAGGCTGCGGCAGGGGGGGCGCtt < 1:4895942/71‑1 (MQ=255)
ccTGGCTGTGAGTAGCTATAGTTGCCAGGTCCGACCGGAGCAGGCTGCGGCAGGGGGGGCGCTTTTCCCCt < 1:4239563/71‑1 (MQ=255)
tGGCTGTGAGTAGCTATAGTTGCCAGGCCCGACCGGAGCAGGCTGCGGCAGGGGGGGCGCTTTTccc > 1:4848596/1‑67 (MQ=255)
tgAGTAGCTATAGTTGCCAGGTCCGACCGGAGCAGGCTGCGGCAGGGGGGGCGCTTTTCCCCTCACCCTa < 1:4885069/70‑1 (MQ=255)
ccAGGTCCGACCGGAGCAGGCTGCGGCAGGGGGGGCGCTTTTCCCCTCACCCTAACCCTCTCCCCAGAgg < 1:5069758/70‑1 (MQ=255)
|
GTAAACAGTACGAACAGATAAACGGTTATTATAATCAACCTGGCTGTGAGTAGCTATAGTTGCCAGGTCCGACCGGAGCAGGCTGCGGCAGGGGGGGCGCTTTTCCCCTCACCCTAACCCTCTCCCCAGAGG > W3110S.gb/1352814‑1352945
|
| 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
