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 |
756,824 |
C→A |
100% |
H84N (CAC→AAC) |
lolE → |
outer membrane‑specific lipoprotein transporter subunit |
|
| |
seq id |
position |
ref |
new |
freq |
score (cons/poly) |
reads |
annotation |
genes |
product |
| * | minE | 756,824 | 0 | C | A | 75.0%
| 51.2
/ 17.7
| 40 | H84N (CAC→AAC) | lolE | outer membrane‑specific lipoprotein transporter subunit |
| Reads supporting (aligned to +/- strand): ref base C (3/7); new base A (0/30); total (3/37) |
| Fisher's exact test for biased strand distribution p-value = 1.21e-02 |
| Kolmogorov-Smirnov test that lower quality scores support variant p-value = 1.00e+00 |
| Rejected as polymorphism: Variant not supported by required number of reads on each strand. |
GTGAAATCGAGGCGGTGGATCAGCCGTGGACTAACTGGCAGGAAGCACTGGATCACGTGCAAAAAGTGCCGGGTATTGCCGCTGCCGCGCCGTATATCAATTTCACCGGGCTGGTGGAAAGTG > minE/756771‑756893
|
gTGAAATTGAGGCGGTAGATCAGCCGTTGACCAACTGGCAGGAAGCACTGGATAACGTGCAGAAAGTGc < 1:2656106/69‑1 (MQ=255)
gTGAAATTGAGGCGGTAGATCAGCCGTGGACCAACTGGCAGGAAGCACTGGATAACGTGCAGTAAGTGc < 1:439973/69‑1 (MQ=255)
gTGAAATTGAGGCGGTAGATCAGCCGTGGACCAACTGGCAGGAAGCACTGGATAACGTGCAGAAAGTGc < 1:1134456/69‑1 (MQ=255)
gTGAAATTGAGGCGGTAGATCAGCCGTGGACCAACTGGCAGGAAGCACTGGATAACGTGCAGAAAGTGc < 1:353259/69‑1 (MQ=255)
gTGAAATTGAGGCGGTAGATCAGCCGTGGACCAACTGGCAGGAAGCACTGGATAACGTGCAGAAAGTGc < 1:3147865/69‑1 (MQ=255)
gTGAAATTGAGGCGGTAGATCAGCCGTGGACCAACTGGCAGGAAGCACTGGATAACGTGCAGAAAGTGc < 1:1442706/69‑1 (MQ=255)
gTGAAATTGAGGCGGTAGATCAGCCGTGGACCAACTGGCAGGAAGCACTGGATAACGTGCAGAAAGTGc < 1:2208094/69‑1 (MQ=255)
gTGAAATTGAGGCGGTAGATCAGCCGTGGACCAACTGGCAGGAAGCACTGGATAACGTGCAGAAAGTGc < 1:1571300/69‑1 (MQ=255)
aTCGAGGCGGTGGATCAGCCGTGGACTAACTGGCAGGAAGCACTGGATCACGTGCAAAAAGTGCCggg < 1:1013386/68‑1 (MQ=255)
aTCGAGGCGGTGGATCAGCCGTGGACTAACTGGCAGGAAGCACTGGATCACGTGCAAAAAGTGCCggg < 1:3047302/68‑1 (MQ=255)
cAGCCGTGGACCAACTGGCAGGAAGCACTGGATAACGTGCAGAAAGTGCCGGGCAtt < 1:1902775/57‑1 (MQ=255)
cAGCCGTGGACCAACTGGCAGGAAGCACTGGATAACGTGCAGAAAGTGCCGGGCAtt < 1:1734598/57‑1 (MQ=255)
cAGCCGTGGACCAACTGGCAGGAAGCACTGGATAACGTGCAGAAAGTGCCGGGCAtt < 1:2064549/57‑1 (MQ=255)
cAGCCGTGGACCAACTGGCAGGAAGCACTGGATAACGTGCAGAAAGTGCCGGGCAtt < 1:2659632/57‑1 (MQ=255)
cAGCCGTGGACCAACTGGCAGGAAGCACTGGATAACGTGCAGAAAGTGCCGGGCAtt < 1:2194064/57‑1 (MQ=255)
cAGCCGTGGACCAACTGGCAGGAAGCACTGGATAACGTGCAGAAAGTGCCGGGCAtt < 1:2327068/57‑1 (MQ=255)
cAGCCGTGGACCAACTGGCAGGAAGCACTGGATAACGTGCAGAAAGTGCCGGGCAtt < 1:2655149/57‑1 (MQ=255)
cAGCCGTGGACCAACTGGCAGGAAGCACTGGATAACGTGCAGAAAGTGCCGGGCAtt < 1:2419307/57‑1 (MQ=255)
cAGCCGTGGACCAACTGGCAGGAAGCACTGGATAACGTGCAGAAAGTGCCGGGCAtt < 1:2600867/57‑1 (MQ=255)
cAGCCGTGGACCAACTGGCAGGAAGCACTGGATAACGTGCAGAAAGTGCCGGGCAtt < 1:1862054/57‑1 (MQ=255)
cAGCCGTGGACCAACTGGCAGGAAGCACTGGATAACGTGCAGAAAGTGCCGGGCAtt < 1:2957536/57‑1 (MQ=255)
cAGCCGTGGACCAACTGGCAGGAAGCACTGGATAACGTGCAGAAAGTGCCGGGCAtt < 1:1775642/57‑1 (MQ=255)
cAGCCGTGGACCAACTGGCAGGAAGCACTGGATAACGTGCAGAAAGTGCCGGGCAtt < 1:1726109/57‑1 (MQ=255)
cAGCCGTGGACCAACTGGCAGGAAGCACTGGATAACGTGCAGAAAGTGCCGGGCAtt < 1:1534650/57‑1 (MQ=255)
cAGCCGTGGACCAACTGGCAGGAAGCACTGGATAACGTGCAGAAAGTGCCGGGCAtt < 1:1423956/57‑1 (MQ=255)
cAGCCGTGGACCAACTGGCAGGAAGCACTGGATAACGTGCAGAAAGTGCCGGGCAtt < 1:1354342/57‑1 (MQ=255)
cAGCCGTGGACCAACTGGCAGGAAGCACTGGATAACGTGCAGAAAGTGCCGGGCAtt < 1:1285697/57‑1 (MQ=255)
cAGCCGTGGACCAACTGGCAGGAAGCACTGGATAACGTGCAGAAAGTGCCGGGCAtt < 1:1239736/57‑1 (MQ=255)
cAGCCGTGGACCAACTGGCAGGAAGCACTGGATAACGTGCAGAAAGTGCCGGGCAtt < 1:1018152/57‑1 (MQ=255)
aGCCGTGGACCAACTGGCAGGAAGCACTGGATAACGTGCAGAAAGTGCCGGGCAtt < 1:2132318/56‑1 (MQ=255)
gCCGTGGACCAACTGGCAGGAAGCACTGGATAACGTGCAGAAAGTGCCGGGCAtt < 1:487119/55‑1 (MQ=255)
gAAGCACTGGATAACGTGCAGAAAGTGCCGGGCAtt < 1:2088036/36‑1 (MQ=25)
aaGCACTGGATCACGTGCAAAAAGTGCCGGGTATTGCCGCTGCCGCGCCGTATATCAATTTCACCGGGc > 1:2339102/1‑69 (MQ=255)
aaGCACTGGATCACGTGCAAAAAGTGCCGGGTATTGCCGCTGCCGCGCCGTATATCAATTTCACCGGGc > 1:947086/1‑69 (MQ=255)
ggATCACGTGCAAAAAGTGCCGGGTATTGCCGCTGCCGCGCCGTATATCAATTTCACCGGGCtggt > 1:2234317/1‑66 (MQ=255)
gATCACGTGCAAAAAGTGCCGGGTATTGCCGCTGCCGCGCCGTATATCAATTTCACCGGGCtg < 1:2529671/63‑1 (MQ=255)
gATCACGTGCAAAAAGTGCCGGGTATTGCCGCTGCCGCGCCGTATATCAATTTCACCGGGCtg < 1:1663510/63‑1 (MQ=255)
gATCACGTGCAAAAAGTGCCGGGTATTGCCGCTGCCGCGCCGTATATCAATTTCACCGGGCtg < 1:3132411/63‑1 (MQ=255)
gATCACGTGCAAAAAGTGCCGGGTATTGCCGCTGCCGCGCCGTATATCAATTTCACCGGGCtg < 1:3324796/63‑1 (MQ=255)
gATCACGTGCAAAAAGTGCCGGGTATTGCCGCTGCCGCGCCGTATATCAATTTCACCGGGCtg < 1:1112397/63‑1 (MQ=255)
cACGTGCAAAAAGTGCCGGGTATTGCCGCTGCCGCGCCGTATATCAATTTCACCGGGCTGGTGGAAAGt > 1:2435963/1‑69 (MQ=255)
cACGTGCAAAAAGTGCCGGGTATTGCCGCTGCCGCGCCGTATATCAATTTCACCGGGCTGGTGGAAAGt > 1:1851718/1‑69 (MQ=255)
cACGTGCAAAAAGTGCCGGGTATTGCCGCTGCCGCGCCGTATATCAATTTCACCGGGCTGGTGGAAAGt > 1:1260152/1‑69 (MQ=255)
cACGTGCAAAAAGTGCCGGGTATTGCCGCTGCCGCGCCGTATATCAATTTCACCGGGCTGGTGGAAAGt > 1:616479/1‑69 (MQ=255)
cACGTGCAAAAAGTGCCGGGTATTGCCGCTGCCGCGCCGTATATCAATTTCACCGGGCTGGT‑GAAAGTg > 1:14214/1‑69 (MQ=255)
|
GTGAAATCGAGGCGGTGGATCAGCCGTGGACTAACTGGCAGGAAGCACTGGATCACGTGCAAAAAGTGCCGGGTATTGCCGCTGCCGCGCCGTATATCAATTTCACCGGGCTGGTGGAAAGTG > minE/756771‑756893
|
| 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
