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 F17 I0 R2
|
162 |
60.6 |
4616657 |
98.5% |
4547407 |
62.1 |
Breseq alignment
BRESEQ :: Evidence
|
| evidence |
seq id |
position |
mutation |
freq |
annotation |
gene |
description |
| RA |
W3110S.gb |
349,140 |
C→T |
12.5% |
intergenic (+344/‑96) |
prpB → / → prpC |
2‑methylisocitrate lyase/2‑methylcitrate synthase |
|
| |
seq id |
position |
ref |
new |
freq |
score (cons/poly) |
reads |
annotation |
genes |
product |
| * | W3110S.gb | 349,140 | 0 | C | T | 12.5%
| 133.4
/ 9.7
| 48 | intergenic (+344/‑96) | prpB/prpC | 2‑methylisocitrate lyase/2‑methylcitrate synthase |
| Reads supporting (aligned to +/- strand): ref base C (19/23); new base T (4/2); total (23/25) |
| Fisher's exact test for biased strand distribution p-value = 4.07e-01 |
| Kolmogorov-Smirnov test that lower quality scores support variant p-value = 1.00e+00 |
ACGCATAGCGTCGCATCCGACAACCGATGCCTGATGCGCCGCTGACGCGACTTATCAGGCCTACGGGGTGAACTGAACTGTAGGTCGGATAAGACGCATAGCGTCGCATCCGACAACAATCTCGACCCTA > W3110S.gb/349080‑349209
|
aCGCATAGCGTCGCATCCGACAACCGATGCCTGATGCGCCGCTGACGCGACTTATCAGGCCTACGGGGtga < 1:3993243/71‑1 (MQ=31)
gCATAGCGTCGCATCCGACAACCGATGCCTGATGCGCCGCTGACGCGACTTATCAGGCTTACGGGGtgagc > 1:71033/1‑69 (MQ=9)
aGCGTCGCATCCGACAACCGATGCCTGATGCGCCGCTGACGCGACTTATCAGGCCTACGGGGtgaactgaa > 1:2523963/1‑71 (MQ=34)
gTCGCATCCGACAACCGATGCCTGATGCGCCGCTGACGCGACTTATCAGGCCTACGGGGTGaactgaactg < 1:4599333/71‑1 (MQ=34)
gCATCCGACAACCGATGCCTGATGCGCCGCTGACGCGACTTATCAGGCCTACGGGGTGAACTGAACTGTAg > 1:3944498/1‑71 (MQ=34)
cATCCGACAACCGATGCCTGATGCGCCGCTGACGCGACTTATCAGGCCTACGGGGTGAACTGAACTGTAgg < 1:1352971/71‑1 (MQ=34)
gACAACCGATGCCTGATGCGCCGCTGACGCGACTTATCAGGCCTACGGGGTGAACTGAACTGTAGGTCGGa < 1:4544203/71‑1 (MQ=34)
cAACCGATGCCTGATGCGCCGCTGACGGGACTTATCAGGCCTACGGGGTGAACTGAACTGTAGGTCGGAt > 1:1589325/1‑70 (MQ=255)
cAACCGATGCCTGATGCGCCGCTGACGCGACTTATCAGGCCTACGGGGTGAACTGAACTGTAGGTCGGATa < 1:76233/71‑1 (MQ=34)
cAACCGATGCCTGATGCGCCGCTGACGCGACTTATCAGGCCTACGGGGTGAACTGAACTGTAGGTCGGATa < 1:2359312/71‑1 (MQ=34)
ccGATGCCTGATGCGCCGCTGACGCGACTTATCAGGCCTACGGGGTGAACTGAACTGTAGGTCGGATAAGa < 1:4238364/71‑1 (MQ=34)
gATGCCTGATGCGCCGCTGACGCGACTTATCAGGCCTACGGGGtga > 1:545251/1‑46 (MQ=32)
tGCCTGATGCGCCGCTGACGCGACTTATCAGGCCTACGGGGTGAACTGAACTGTAGGTCGGATAAGACGCa < 1:2215149/71‑1 (MQ=34)
tGCCTGATGCGCCGCTGACGCGACTTATCAGGCCTACGGGGTGAACTGAACTGTAGGTCGGATAAGACGCa > 1:3591795/1‑71 (MQ=34)
gCCTGATGCGCCGCTGACGCGACTTATCAGGCCTACGGGGtgaact > 1:3073493/1‑46 (MQ=38)
ccTGATGCGCCGCTGACGCGACTTATCAGGCCTACGGGGTGAACTGAACTGTAGGTCGGATAAGACGCATa < 1:3615339/71‑1 (MQ=34)
ccTGATGCGCCGCTGACGCGACTTATCAGGCCTACGGGGTGAACTGAACTGTAGGTCGGATAAGACGCATa < 1:1153485/71‑1 (MQ=34)
tGATGCGCCGCTGACGCGACTTATCAGGCCTACGGGGTGAACTGAACTGTAGGTCGGATAAGACGc < 1:349169/66‑1 (MQ=35)
tGATGCGCCGCTGACGCGACTTATCAGGCCTACGGGGTGAACTGAACTGTAGGTCGGATAAGACGCATa < 1:1011521/69‑1 (MQ=35)
gATGCGCCGCTGACGCGACTTATCAGGCCTACGGGGTGAACTGAACTGTAGGTCGGATAAGACGCATAGCg > 1:4398223/1‑71 (MQ=34)
aTGCGCCGCTGACGCGACTTATCAGGCTTACGGGGTGAACTGAACTGTAGGTCGGATAAGACGCATAGCg < 1:1691203/70‑1 (MQ=25)
aTGCGCCGCTGACGCGACTTATCAGGCTTACGGGGTGAACTGAACTGTAGGTCGGATAAGACGCATAGCGt > 1:4180688/1‑71 (MQ=21)
aTGCGCCGCTGACGCGACTTATCAGGCTTACGGGGTGAACTGAACTGTAGGTCGGATAAGACGCATAGCGt > 1:3549995/1‑71 (MQ=21)
aTGCGCCGCTGACGCGACTTATCAGGCCTACGGGGTGAACTGAACTGTAg > 1:3268360/1‑50 (MQ=38)
aTGCGCCGCTGACGCGACTTATCAGGCCTACGGGGTGAACTGAACTGTAGGTCGGATAAGACGCATAGCg < 1:1856628/70‑1 (MQ=35)
gcgcCGCTGACGCGACTTATCAGGCCTACGGGGTGAACTGAACTGt < 1:3557227/46‑1 (MQ=38)
gcgcCGCTGACGCGACTTATCAGGCCTACGGGGTGAACTGAACTGTAGGTCGGATAAGACGCATAGCGTCg > 1:1776299/1‑71 (MQ=34)
gccgcTGACGCGACTTATCAGGCCTACGGGGtgaactg < 1:532251/38‑1 (MQ=40)
gccgcTGACGCGACTTATCAGGCCTACGGGGtgaactg < 1:1047033/38‑1 (MQ=40)
gccgcTGACGCGACTTATCAGGCCTACGGGGTGAACTGAACTGTAGGTCGGATAAGACGCATAGCGTCGCa < 1:2023738/71‑1 (MQ=34)
ccgcTGACGCGACTTATCAGGCCTACGGGGTGAACTGAACTGTAGGTCGGa > 1:3148038/1‑51 (MQ=35)
gcTGACGCGACTTATCAGGCCTACGGGGTGAACTGAACTGTAGGTCGGATAAGACGCATAGCGTCGCATcc < 1:1845842/71‑1 (MQ=34)
cTGACGCGACTTATCAGGCCTACGGGGTGAACTGAACTGTAGGTCGGATAAGACGCATAGCGTCGCATcc > 1:2917295/1‑70 (MQ=35)
gACGCGACTTATCAGGCCTACGGGGTGAACTGAACTGTAGGTCGGATAAGACGCATAGCGTCGCATCCg < 1:3843111/69‑1 (MQ=35)
gACGCGACTTATCAGGCCTACGGGGTGAACTGAACTGTAGGTCGGATAAGACGCATAGCGTCGCATCCGa > 1:4593603/1‑70 (MQ=35)
aCGCGACTTATCAGGCCTACGGGGTGAACTGAACTGTAGGTCGGATAAGACGCATAGCGTCGCATCCGac < 1:1254062/70‑1 (MQ=35)
gcgACTTATCAGGCCTACGGGGTGAACTGATCTGTAGGTCGGATAAGACGCATAGCGTCGCATCCGacaa > 1:3410956/1‑70 (MQ=25)
gACTTATCAGGCCTACGGGGTGAACTGAACTGTAGGTCGGATAAGACGCATAGCGTCGCATCCGac < 1:2345099/66‑1 (MQ=35)
gACTTATCAGGCCTACGGGGTGAACTGAACTGTAGGTCGGATAAGACGCATAGCGTCGCATCCGAcaacaa > 1:4257139/1‑71 (MQ=38)
gACTTATCAGGCCTACGGGGTGAACTGAACTGTAGGTCGGATAAGACGCATAGCGTCGCATCCGAcaacaa > 1:2067432/1‑71 (MQ=38)
cTTATCAGGCCTACGGGGTGAACTGAACTGTAGGTCGGATAAGACGCATAGCGTCGCATCCGACAACAAtc > 1:4483802/1‑71 (MQ=40)
ttATCAGGCTTACGGGGTGAACTGAACTGTAGGTCGGATAAGACGCATAGCg < 1:2857563/52‑1 (MQ=255)
ttATCAGGCCTACGGGGTGAACTGAACTGTAGGTCGGATAAGACGCATAGCGTCGCATCCGACAACAAtct > 1:3486763/1‑71 (MQ=255)
ttATCAGACCTACGGGGTGAACTGAACTGTAGGTCGGATAAGACGCATAGCGTCGCATCCGACAACAAtct > 1:2505537/1‑71 (MQ=255)
aTCAGGCTTACGGGGTGAACTGAACTGTAGGTCGGATAAGACGCATAGCGTCGCATc > 1:528617/1‑57 (MQ=255)
aTCAGGCCTACGGGGTGAACTGAACTGTAGGTCGGATAAGACGCATAGCGTCGCATCCGACAACAAtctc > 1:392334/1‑70 (MQ=255)
tCAGGCCTACGGGGTGAACTGAACTGTAGGTCGGATAAGACGCATAGCGTCGCATCCGACAACAATCTCGa < 1:734680/71‑1 (MQ=255)
aGGCCTACGGGGTGAACTGAACTGTAGGTCGGATAAGACGCATAGCGTCGCATCCGACAACAATCTCGAcc < 1:3152602/71‑1 (MQ=255)
cTACGGGTTGAACTGAACTGTAGGTCGGATAAGACGCATAGCGTCGCATCCGACAACAATCTCGACCCTa > 1:35022/1‑70 (MQ=255)
cTACGGGGTGAACTGAACTGTAGGTCGGATAAGACGCATAGCGTCGCATCCGACAACAATCTCGACCCTa > 1:1261690/1‑70 (MQ=255)
|
ACGCATAGCGTCGCATCCGACAACCGATGCCTGATGCGCCGCTGACGCGACTTATCAGGCCTACGGGGTGAACTGAACTGTAGGTCGGATAAGACGCATAGCGTCGCATCCGACAACAATCTCGACCCTA > W3110S.gb/349080‑349209
|
| 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
