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 |
|
A6 F21 I0 R1
|
2169 |
63.0 |
3952800 |
76.2% |
3012033 |
62.4 |
Breseq alignment
BRESEQ :: Evidence
|
| evidence |
seq id |
position |
mutation |
freq |
annotation |
gene |
description |
| RA |
minE |
259,095 |
T→C |
20.9% |
Y8H (TAT→CAT) |
yajD → |
conserved hypothetical protein |
|
| |
seq id |
position |
ref |
new |
freq |
score (cons/poly) |
reads |
annotation |
genes |
product |
| * | minE | 259,095 | 0 | T | C | 20.9%
| 81.3
/ 17.9
| 43 | Y8H (TAT→CAT) | yajD | conserved hypothetical protein |
| Reads supporting (aligned to +/- strand): ref base T (18/16); new base C (2/7); total (20/23) |
| Fisher's exact test for biased strand distribution p-value = 1.42e-01 |
| Kolmogorov-Smirnov test that lower quality scores support variant p-value = 9.52e-01 |
CATCTTGGGAAACTGCGCGTAACCCTACATTTCATCCAGGTAACTTTTCATGGCTATCATCCCAAAAAACTATGCGCGGTTAGAAAGCGGCTATCGCGAAAAAGCATTAAAAATCTATCCGTGGGTCTGCGGTCGCT > minE/259025‑259161
|
cATCTTGGGAAACTGCGCGTAACCCTACATTTCATCCAGGTAACTTTTCATGGCTATCATCCCAAAAAACt < 1:2385394/71‑1 (MQ=255)
gggAAACTGCGCGTAACCCTACATTTCATCCAGGTAACTTTTCATGGCTATCATCCCAAAAAACCATgcg < 1:3157433/70‑1 (MQ=255)
ggAAACTGCGCGTAACCCTACATTTCATCCAGGTAACTTTTCATGGCTATCATCCCAAAAAACTATgcgc < 1:1375976/70‑1 (MQ=255)
ggAAACTGCGCGTAACCCTACATTTCATCCAGGTAACTTTTCATGGCTATCATCCCAAAAAACTATGcgcg < 1:3506731/71‑1 (MQ=255)
cgcgTAACCCTACATTTCATCCAGGTAACTTTTCATGGCTATCATCCCAAAAAACTATGCGCGGTTAGa > 1:730837/1‑69 (MQ=255)
aaCCCTACATTTCATCCAGGTAACTTTTCATGGCTATCATCCCAAAAAACTATGCGCGGTTAGAAAGCGGc > 1:3533440/1‑71 (MQ=255)
aaCCCTACATTTCATCCAGGTAACTTTTCATGGCTATCATCCCAAAAAACTATGCGCGGTTAGAAAGCGGc > 1:3242970/1‑71 (MQ=255)
cccTACATTTCATCCAGGTAACTTTTCATGGCTATCATCCCAAAAAACCATGCGCGGTTAGaaa < 1:2640589/64‑1 (MQ=255)
ccTACATTTCATCCAGGTAACTTTTCATGGCTATCATCCCAAAAAACTAt < 1:1370997/50‑1 (MQ=255)
ccTACATTTCATCCAGGTAACTTTTCATGGCTATCATCCCAAAAAACTATGCGCGGTTAGAAAGCGGCTAt < 1:1900245/71‑1 (MQ=255)
cTACATTTCATCCAGGTAACTTTTCATGGCTATCATCCCAAAAAACTATgc < 1:2598012/51‑1 (MQ=255)
cTACATTTCATCCAGGTAACTTTTCATGGCTATCATCCCAAAAAACTATGCGCGGTTAGAAAGCGGCTATc < 1:679031/71‑1 (MQ=255)
cTACATTTCATCCAGGTAACTTTTCATGGCTATCATCCCAAAAAACCATGCGCGGTTAGAAAGCGGCTa < 1:265470/69‑1 (MQ=255)
cTACATTTCATCCAGGTAACTTTTCATGGCTATCATCCCAAAAAACCATGCGCGGTTAGAAAGCGGCTa < 1:2201902/69‑1 (MQ=255)
tACATTTCATCCAGGTAACTTTTCATGGCTATCATCCCAAAAAACTATgcg > 1:3800851/1‑51 (MQ=255)
tACATTTCATCCAGGTAACTTTTCATGGCTATCATCCCAAAAAACTATGCGCGGTTAGAAAg < 1:1299603/62‑1 (MQ=255)
ttCATCCAGGTAACTTTTCATGGCTATCATCCCAAAAAACTATGCGCGGTTAGAAAGCGGCTAt > 1:3731664/1‑64 (MQ=255)
ggTAACTTTTCATGGCTATCATCCCAAAAAACTATGCGCGGTTAGAAAGCGGCTATCGCGAAAAAGCATTa < 1:1338461/71‑1 (MQ=255)
tAACTTTTCATGGCTATCATCCCAAAAAACTATGCGCGGTTAGAAAGCGGCTATCGCGAAAAAGCATTaa > 1:1827826/1‑70 (MQ=255)
tAACTTATCATGGCTATCATCCCAAAAAACTATGCGCGGTTAGAAAGCGGCTATCGCGAAAAAGCATTaa > 1:8604/1‑70 (MQ=255)
aaCTTTTCATGGCTATCATCCCAAAAAACTATGCGCGGTTAGAAAGCGGCTATCGCGaaa > 1:155694/1‑60 (MQ=255)
aCTTTTCATGGCTATCATCCCAAAAAACTATGCGCGGTTAGAAAGCGGCTATCGCGAAAAAGCATTaaaaa < 1:1981798/71‑1 (MQ=255)
aCTTTTCATGGCTATCATCCCAAAAAACTATGCGCGGTTAGAAAGCGGCTATCGCGAAAAAGCATTaaaaa > 1:3511325/1‑71 (MQ=255)
aCTTTTCATGGCTATCATCCCAAAAAACCATGCGCGGTTAGAAAGCGGCTATCGCGAAAAAGCATTaaaa < 1:560291/70‑1 (MQ=255)
cTTTTCATGGCTATCATCCCAAAAAACTATGCGCGGTTAGAAAGCGGCTATCGCGAAAAAg < 1:1476659/61‑1 (MQ=255)
cTTTTCATGGCTATCATCCCAAAAAACTATGCGCGGTTAGAAAGCGGCTATCGCGAAAAAGCATTAAAAAt > 1:3216389/1‑71 (MQ=255)
ttCATGGCTATCATCCCAAAAAACTATGCGCGGtt > 1:3160551/1‑35 (MQ=255)
ttCATGGCTATCATCCCAAAAAACTATGCGCGGtt > 1:3882110/1‑35 (MQ=255)
ttCATGGCTATCATCCCAAAAAACTATGCGCGGTTAGa > 1:569490/1‑38 (MQ=255)
ttCATGGCTATCATCCCAAAAAACTATGCGCGGTTAGAAAGCGGCTAt > 1:1823650/1‑48 (MQ=255)
ttCATGGCTATCATCCCAAAAAACTATGCGCGGTTAGAAAGCGGCTATCGCGAAAAAGCATTAAAAATCTa > 1:1995713/1‑71 (MQ=255)
ttCATGGCTATCATCCCAAAAAACCATGCGCGGTTAGAAAGCGGCTATCGCGAAAAAGc > 1:2817665/1‑59 (MQ=255)
cATGGCTATCATCCCAAAAAACTATGCGCGGTTAGAAAGCGGCTATCGCGAAAAAGCATTAAAAATCTAt < 1:2634553/70‑1 (MQ=255)
aTGGCTATCATCCCAAAAAACTATGCGCGGTTAGaa < 1:3082511/36‑1 (MQ=255)
tGGCTATCATCCCAAAAAACCATGCGCGGTTAGAAATCGGCTATCGCGAAAAAGCATTAAAAATCTATCCg < 1:2751733/71‑1 (MQ=255)
tGGCTATCATCCCAAAAAACCATGCGCGGTTAGAAAGCGGCTATCGCGAAAAAGCATTAAAAATCTAt < 1:1240025/68‑1 (MQ=255)
tATCATCCCAAAAAACTATGCGCGGTTAGAAAGCGGCTATCGCGAAAAAGCATTAAAAATCTATCCGTggg > 1:2762907/1‑71 (MQ=255)
atcCCAAAAAACTATGCGCGGTTAGAAAGCGGCTATCGCGAAAAAGCATTAAAAATCTATCCGTGGGTCTg < 1:2937042/71‑1 (MQ=255)
cccAAAAAACTATGCGCGGTTAGAAAGCGGCTATCGCGAAAAAGCATTAAAAATCTATCCGTGGGTCTGCg > 1:1023728/1‑71 (MQ=255)
cAAAAAACTATGCGCGGTTAGAAAGCGGCTATCGCGAAAAAGCATTAAAAATCTATCCGTGGGTCTGCGGt < 1:3657836/71‑1 (MQ=255)
aaaaaCTATGCGCGGTTAGAAAGCGGCTATCGCGAAAAAGCATTAAAAATCTATCCGTGGGTCTGCGGTCg < 1:2477769/71‑1 (MQ=255)
aaaaCTATGCGCGGTTAGAAAGCGGCTATCGCGAAAAAGCATTAAAAATCTATCCGTGGGTCTGCGGTCGc > 1:2816635/1‑71 (MQ=255)
aaaCCATGCGCGGTTAGAAAGCGGCTATCGCGAAAAAGCATTAAAAATCTATCCGTGGGTCTGCGGTCGCt > 1:3704643/1‑71 (MQ=255)
aaCTATGCGCGGTTAGAAAGCGGCTATCGCGAAAAAGCATTAAAAATCTATCCg < 1:3419551/54‑1 (MQ=255)
|
CATCTTGGGAAACTGCGCGTAACCCTACATTTCATCCAGGTAACTTTTCATGGCTATCATCCCAAAAAACTATGCGCGGTTAGAAAGCGGCTATCGCGAAAAAGCATTAAAAATCTATCCGTGGGTCTGCGGTCGCT > minE/259025‑259161
|
| 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
