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 |
2,612,535 |
T→G |
68.2% |
S330R (AGC→CGC) |
nikA ← |
nickel transporter subunit |
|
| |
seq id |
position |
ref |
new |
freq |
score (cons/poly) |
reads |
annotation |
genes |
product |
| * | minE | 2,612,535 | 0 | T | G | 68.2%
| 56.5
/ 26.1
| 47 | S330R (AGC→CGC) | nikA | nickel transporter subunit |
| Reads supporting (aligned to +/- strand): ref base T (6/9); new base G (13/19); total (19/28) |
| Fisher's exact test for biased strand distribution p-value = 1.00e+00 |
| Kolmogorov-Smirnov test that lower quality scores support variant p-value = 1.00e+00 |
CCGCAGGCAGCGTCCAACCGGCTTTTTCCAGCAACGCTTTCGCTTTTTGCGGATCGTACTGGCTCGGTTTCAGGCCGAGGTTGGCGTAGGGCACAGAAGGGGCAAACAGGGTGTCGGCGACCTGCTGGG > minE/2612472‑2612600
|
ccGCAGGCAGCGTCCAACCGGCTTTTTCCAGCAACGCTTTCGCTTTTTGCGGATCGTACTGGCTCGGt < 1:2145660/68‑1 (MQ=255)
ccGCAGGCAGCGTCCAACCGGCTTTTTCCAGCAACGCTTTCGCTTTTTGCGGATCGTACTGGCTCGGt < 1:1832337/68‑1 (MQ=255)
ccGCAGGCAGCGTCCAACCGGCTTTTTCCAGCAACGCTTTCGCTTTTTGCGGATCGTACTGGCTCGGt < 1:1682460/68‑1 (MQ=255)
gcaggcagCGTCCAAGCGGCTTTTTCCAGCAACGCTTTCGCTTTCTGCGGATCGTACTGGGGCGGTTTc > 1:3191388/1‑69 (MQ=255)
gcaggcagCGTCCAACGGGCTTTTTCCAGCAACGCTTTCGCTTTCTGCGGATCGTACTGGCGCGGTTTc > 1:2221791/1‑69 (MQ=255)
gcaggcagCGTCCAACCGGCTTTTTCCAGCAACGCTTTCGCTTTCTGCGGATCGTACTGGCGCGGt > 1:1213528/1‑66 (MQ=255)
gcaggcagCGTCCAACCGGCTTTTTCCAGCAACGCTTTCGCTTTCTGCGGATCGTACTGGCGCGGTTTc > 1:2218300/1‑69 (MQ=255)
gcaggcagCGTCCAACCGGCTTTTTCCAGCAACGCTTTCGCTTTCTGCGGATCGTACTGGCGCGGTTTc > 1:778699/1‑69 (MQ=255)
gcaggcagCGTCCAACCGGCTTTTTCCAGCAACGCTTTCGCTTTCTGCGGATCGTACTGGCGCGGTTTc > 1:360879/1‑69 (MQ=255)
gcaggcagCGTCCAACCGGCTTTTTCCAGCAACGCTTTCGCTTTCTGCGGATCGTACTGGCGCGGTTTc > 1:3195300/1‑69 (MQ=255)
gcaggcagCGTCCAACCGGCTTTTTCCAGCAACGCTTTCGCTTTCTGCGGATCGTACTGGCGCGGTTTc > 1:1905913/1‑69 (MQ=255)
gcaggcagCGTCCAACCGGCTTTTTCCAGCAACGCTTTCGCTTTCTGCGGATCGTACTGGCGCGGTTTc > 1:1157630/1‑69 (MQ=255)
gcaggcagCGTCCAACCGGCTTTTTCCAGCAACGCTTTCGCTTTCTGCGGATCGTACTGGCGCGGTTTc > 1:1247040/1‑69 (MQ=255)
gcaggcagCGTCCAACCGGCTTTTTCCAGCAACGCTTTCGCTTTCTGCGGATCGTACTGGCGCGGTTTc > 1:1196242/1‑69 (MQ=255)
gcaggcagCGTCCAACCGGCTTTTTCCAGCAACGCTTTCGCTTTCTGCGGATCGTACTGGCGCGGTTTc > 1:1547463/1‑69 (MQ=255)
gcaggcagCGTCCAACCGGCTTTTTCCAGCAACGCTTTCGCTTTCTGCGGATCGTACTGGCGCGGTTTc > 1:1564594/1‑69 (MQ=255)
aggcagCGTCCAACCGGCTTTTTCCAGCAACGCTTTCGCTTTTTGCGGATCGTACTGGCTCGGTTTCAg < 1:1610148/69‑1 (MQ=255)
ccAACCGGCTTTTTCCAGCAACGCTTTCGCTTTTTGCGGATCGTACTGGCTCGGTTTCAGGCCGAGGtt < 1:3043251/69‑1 (MQ=255)
ccAACCGGCTTTTTCCAGCAACGCTTTCGCTTTTTGCGGATCGTACTGGCTCGGTTTCAGGCCGAGGtt < 1:3189841/69‑1 (MQ=255)
ccAACCGGCTTTTTCCAGCAACGCTTTCGCTTTTTGCGGATCGTACTGGCTCGGTTTCAGGCCGAGGtt < 1:2534058/69‑1 (MQ=255)
cAACCGGCTTTTTCCAGCAACGCTTTCGCTTTTTGCGGATCGTACTGGCTCGGTTTCAGGCCGAGGTTg > 1:1842685/1‑69 (MQ=255)
cAACCGGCTTTTTCCAGCAACGCTTTCGCTTTTTGCGGATCGTACTGGCTCGGTTTCAGGCCGAGGTTg > 1:490485/1‑69 (MQ=255)
cAACCGGCTTTTTCCAGCAACGCTTTCGCTTTTTGCGGATCGTACTGGCTCGGTTTCAGGCCGAGGTTg > 1:1954873/1‑69 (MQ=255)
cAACCGGCTTTTTCCAGCAACGCTTTCGCTTTTTGCGGATCGTACTGGCTCGGTTTCAGGCCGAGGTTg > 1:665046/1‑69 (MQ=255)
ccGGCTTTTTCCAGCAACGCTTTCGCTTTTTGCGGATCGTACTGGCTCGGTTTCAGGCCGAGGTTGGCg < 1:3372116/69‑1 (MQ=255)
ccGGCTTTTTCCAGCAACGCTTTCGCTTTTTGCGGATCGTACTGGCTCGGTTTCAGGCCGAGGTTGGCg < 1:643296/69‑1 (MQ=255)
gCTTTTTCCAGCAACGCTTTCGCTTTTTGCGGATCGTACTGGCTCGGTTTCAGGCCGAGGTTg > 1:232734/1‑63 (MQ=255)
gctttcgctttcTGCGGATCGTACTGGCGCGGTTTCAGTCCGAGGTTGGCGTAGGGCACAGAAGGGGCa < 1:1076913/69‑1 (MQ=255)
gctttcgctttcTGCGGATCGTACTGGCGCGGTTTCAGGCCGAGGTTGGCGTAGGGCACAGAAGGGGCa < 1:665753/69‑1 (MQ=255)
gctttcgctttcTGCGGATCGTACTGGCGCGGTTTCAGGCCGAGGTTGGCGTAGGGCACAGAAGGGGCa < 1:2694327/69‑1 (MQ=255)
gctttcgctttcTGCGGATCGTACTGGCGCGGTTTCAGGCCGAGGTTGGCGTAGGGCACAGAAGGGGCa < 1:57122/69‑1 (MQ=255)
gctttcgctttcTGCGGATCGTACTGGCGCGGTTTCAGGCCGAGGTTGGCGTAGGGCACAGAAGGGGCa < 1:1353337/69‑1 (MQ=255)
gctttcgctttcTGCGGATCGTACTGGCGCGGTTTCAGGCCGAGGTTGGCGTAGGGCACAGAAGGGGCa < 1:3080332/69‑1 (MQ=255)
gctttcgctttcTGCGGATCGTACTGGCGCGGTTTCAGGCCGAGGTTGGCGTAGGGCACAGAAGGGGCa < 1:2937715/69‑1 (MQ=255)
gctttcgctttcTGCGGATCGTACTGGCGCGGTTTCAGGCCGAGGTTGGCGTAGGGCACAGAAGGGGCa < 1:2891121/69‑1 (MQ=255)
gctttcgctttcTGCGGATCGTACTGGCGCGGTTTCAGGCCGAGGTTGGCGTAGGGCACAGAAGGGGCa < 1:2772925/69‑1 (MQ=255)
gctttcgctttcTGCGGATCGTACTGGCGCGGTTTCAGGCCGAGGTTGGCGTAGGGCACAGAAGGGGCa < 1:2768722/69‑1 (MQ=255)
gctttcgctttcTGCGGATCGTACTGGCGCGGTTTCAGGCCGAGGTTGGCGTAGGGCACAGAAGGGGCa < 1:2460360/69‑1 (MQ=255)
gctttcgctttcTGCGGATCGTACTGGCGCGGTTTCAGGCCGAGGTTGGCGTAGGGCACAGAAGGGGCa < 1:138524/69‑1 (MQ=255)
gctttcgctttcTGCGGATCGTACTGGCGCGGTTTCAGGCCGAGGTTGGCGTAGGGCACAGAAGGGGCa < 1:2197618/69‑1 (MQ=255)
gctttcgctttcTGCGGATCGTACTGGCGCGGTTTCAGGCCGAGGTTGGCGTAGGGCACAGAAGGGGCa < 1:2152065/69‑1 (MQ=255)
gctttcgctttcTGCGGATCGTACTGGCGCGGTTTCAGGCCGAGGTTGGCGTAGGGCACAGAAGGGGCa < 1:1539259/69‑1 (MQ=255)
gctttcgctttcTGCGGATCGTACTGGCGCGGTTTCAGGCCGAGGTTGGCGTAGGGCACAGAAGGGGCa < 1:1853269/69‑1 (MQ=255)
gctttcgctttcTGCGGATCGTACTGGCGCGGTTTCAGGCCGAGGTTGGCGTAGGGCACAGAAGGGGCa < 1:1567744/69‑1 (MQ=255)
gctttcgctttcTGCGGATCGTACTGGCGCGGTTTCAGGCCGAGGTTGGCGTAGGGCACAGAAGGGGCa < 1:1672587/69‑1 (MQ=255)
gctttcgctttcTGCGGATCGTACTGGCGCGGTTTCAGGCCGAGGTTGGCGTAGGGCACAGAAGGGGCa < 1:1614356/69‑1 (MQ=255)
ggCTCGGTTTCAGGCCGAGGTTGGCGTAGGGCACAGAAGGGGCAAACAGGGTGTCTGCGACCTGCTggg > 1:2556787/1‑69 (MQ=255)
|
CCGCAGGCAGCGTCCAACCGGCTTTTTCCAGCAACGCTTTCGCTTTTTGCGGATCGTACTGGCTCGGTTTCAGGCCGAGGTTGGCGTAGGGCACAGAAGGGGCAAACAGGGTGTCGGCGACCTGCTGGG > minE/2612472‑2612600
|
| Alignment Legend |
|---|
Aligned base mismatch/match (shaded by quality score): ATCG/ATCG < 3 ≤ ATCG/ATCG < 21 ≤ ATCG/ATCG < 32 ≤ ATCG/ATCG < 36 ≤ ATCG/ATCG |
Unaligned base: atcg Masked matching base: atcg Alignment gap: ‑ Deleted base: ‑ |
GATK/CNVnator alignment
N/A
