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 |
2,970,436 |
C→T |
25.4% |
*215* (TGA→TAA) |
ytjB ← |
conserved hypothetical protein |
|
| |
seq id |
position |
ref |
new |
freq |
score (cons/poly) |
reads |
annotation |
genes |
product |
| * | minE | 2,970,436 | 0 | C | T | 25.4%
| 92.8
/ 31.7
| 55 | *215* (TGA→TAA) | ytjB | conserved hypothetical protein |
| Reads supporting (aligned to +/- strand): ref base C (19/22); new base T (9/5); total (28/27) |
| Fisher's exact test for biased strand distribution p-value = 3.55e-01 |
| Kolmogorov-Smirnov test that lower quality scores support variant p-value = 9.48e-01 |
TCGTAAGAGTCAGAGATGAGCAGGCGTAATGTGGACATAACGATTTCCTTTCTTGTAGTAATGGGTCACTCTTTTTTCTCGCTTTCTTCCTCTTCCGGCACCGGTTTGCTGGCGGTTAACAGGAAGGGCGATTGCT > minE/2970370‑2970505
|
tCGTAAGAGTCAGAGATGAGCAGGCGTAATGTGGACATAACGATTTCCTTTCTTGTAGTAATGGGTCActc < 1:641871/71‑1 (MQ=255)
gTAAGAGTCAGAGATGAGCAGGCGTAATGTGGACATAACGATTTCCTTTCTTGTAGTAATGGGTTACTCtt > 1:2524643/1‑71 (MQ=255)
agagTCAGAGATGAGCAGGCGTAATGTGGACATAACGATTTCCTTTCTTGTAGTAATGGGTTACTCttttt > 1:261539/1‑71 (MQ=255)
gagTCAGAGATGAGCAGGCGTAATGTGGACATAACGATTTCCTTTCTTGTAGTAATGGGTCACTCtttttt < 1:3515712/71‑1 (MQ=255)
gagTCAGAGATGAGCAGGCGTAATGTGGACATAACGATTTCCTTTCTTGTAGTAATGGGTCACTCtttttt > 1:417976/1‑71 (MQ=255)
gagTCAGAGATGAGCAGGCGTAATGTGGACATAACGATTTCCTTTCTTGTAGTAATGGGTCACTCttttt > 1:413211/1‑70 (MQ=255)
tCAGAGATGAGCAGGCGTAATGTGGACATAACGATTTCCTTTCTTGTAGTAATGGGTCACTCTTTTTtctc < 1:2180019/71‑1 (MQ=255)
tCAGAGATGAGCAGGCGTAATGTGGACATAACGATTTCCTTTCTTGTAGTAATGGGTCACTCTTTTTtctc < 1:3192573/71‑1 (MQ=255)
ttGAGCAGGCGTAATGTGGACATAACGATTTCCTTTCTTGTAGTAATGGGTCACTCTTTTTTCTCGCTttc < 1:742373/70‑1 (MQ=255)
aTGAGCAGGCGTAATGTGGACATAACGATTTCCTTTCTTGTAGTAATGGGTTACTCtttt > 1:1568389/1‑60 (MQ=255)
aGCAGGCGTAATGTGGACATAACGATTTCCTTTCTTGTAGTAATGGGTCACTCTTTTTTCTCGCTttctt < 1:3855484/70‑1 (MQ=255)
aGCAGGCGTAATGTGGACATAACGATTTCCTTTCTTGTAGTAATGGGTCACTCTTTTTTCTCGCTttctt < 1:3564407/70‑1 (MQ=255)
ggCGTAATGTGGACATAACGATTTCCTTTCTTGTAGTAATGGGTTACTCTTTTTTCTCGCTTtcttcctct < 1:339371/71‑1 (MQ=255)
gCGTAATGTGGACATAACGATTTCCTTTCTTGTAGTAATGGGTCActc < 1:2015844/48‑1 (MQ=255)
cGTAATGTGGACATAACGATTTCCTTTCTTGTAGTAATGGGTCACTCTTTTTTCTCGCTTtcttcctcttc < 1:2430023/71‑1 (MQ=255)
gTAATGTGGACATAACGATTTCCTTTCTTGTAGTAATGGGTCACTCtttt > 1:2955036/1‑50 (MQ=255)
gTAATGTGGACATAACGATTTCCTTTCTTGTAGTAATGGGTCACTCTTTTTTCTCGCTttc < 1:173174/61‑1 (MQ=255)
gTAATGTGGACATAACGATTTCCTTTCTTGTAGTAATGGGTCACTCTTTTTTCTCGCTTtcttcct > 1:270940/1‑66 (MQ=255)
tAATGTGGACATAACGATTTCCTTTCTTGTAGTAATGGGTCACTCTTTTTTCTCGCTttctt > 1:1372033/1‑62 (MQ=255)
aaTGTGGACATAACGATTTCCTTTCTTGTAGTAATGGGTCACTCTTTTTtct > 1:2097391/1‑52 (MQ=255)
aTGTGGACATAACGATTTCCTTTCTTGTAGTAATGGGTTACTCTTTTTTCTCGCTTTCTTCCTCTTCCgg < 1:2584647/70‑1 (MQ=255)
aTGTGGACATAACGATTTCCTTTCTTGTAGTAATGGGTCACTCTTTTTTCTCGCTTTCTTCCTCTTCCgg < 1:3563793/70‑1 (MQ=255)
tgGACATAACGATTTCCTTTCTTGTAGTAATGGGTCACTCTTTTTTCTCGCTTTCTTCCTCTTCCGGCAc < 1:978718/70‑1 (MQ=255)
ggACATAACGATTTCCTTTCTTGTAGTAATGGGTTACTCTTTTTTCTCGCTTTCTTCCTCTTCCGGCACCg > 1:1696541/1‑71 (MQ=255)
ggACATAACGATTTCCTTTATTGTAGTAATGGGTTActc > 1:1669426/1‑39 (MQ=37)
gACATAACGATTTCCTTTCTTGTAGTAATGGGTCACTCTTTTTTCTCGCTTTCTTCCTCTTCCGGCACCgg > 1:1235767/1‑71 (MQ=255)
aCATAACGATTTCCTTTCTTGTAGTAATGGGTTACTCTTTTTTCTCGCTTTCTTCCTCTTCCGGCACCGGt < 1:3448803/71‑1 (MQ=255)
aTAACGATTTCCTTTCTTGTAGTAATGGGTTACTCTTTTTTCTCGCTTTCTTCCTCTTCCGGCACCGGttt > 1:2816425/1‑71 (MQ=255)
tAACGATTTCCTTTCTTGTAGTAATGGGTCACTCTTTTTTCTCGCTTTCTTCCTCTTCCGGCAc < 1:3370983/64‑1 (MQ=255)
aaCGATTTCCTTTCTTGTAGTAATGGGTCACTCTTTTTTCTCGCTTTCTTCCTCTTCCGGCACCGGTTTGc > 1:2919870/1‑71 (MQ=255)
aaCGATTTCCTTTCTTGTAGTAATGGGTCACTCTTTTTTCTCGCTTTCTTCCTCTTCCGGCACCGGTTTGc > 1:3854603/1‑71 (MQ=255)
aCGATTTCCTTTCTTGTAGTAATGGGTTACTCTTTTTTCTCGc < 1:3740621/43‑1 (MQ=255)
cGATTTCCTTTCTTGTAGTAATGGGTTACTCTTTTTTCTCGCTTtcttcctcttcc > 1:216015/1‑56 (MQ=255)
cGATTTCCTTTCTTGTAGTAATGGGTTACTCTTTTTTCTCGCTTTCTTCCTCTTCCGGCACCGGTTTGCTg > 1:2731430/1‑71 (MQ=255)
gATTTCCTTTCTTGTAGTAATGGGTCACTCTTTTTTCTCGCTTTCTTCCTCTTCCGGCACCGGTTTGCTgg < 1:3471206/71‑1 (MQ=255)
tttCCTTTCTTGTAGTAATGGGTCACTCTTTTTTCTCGCTTtcttcctc > 1:1509648/1‑49 (MQ=255)
tttCCTTTCTTGTAGTAATGGGTCACTCTTTTTTCTCGCTTTCTTCCTCTTCCGGCACCGGTTTGCTGGCg > 1:251717/1‑71 (MQ=255)
tttCTTGTAGTAATGGGTCACTCTTTTTTCTCGCTTTCTTCCTCTTCCGGCACCGGTTTGCTGGCGGTTaa > 1:114495/1‑71 (MQ=255)
tCTTGTAGTAATGGGTCACTCTTTTTTCTCGCTTTCTTCCTCTTCCGGCACCGGTTTGCTGGCGGTTaa > 1:2767575/1‑69 (MQ=255)
tCTTGTAGTAATGGGTCACTCTTTTTTCTCGCTTTCTTCCTCTTCCGGCACCGGTTTGCTGGCGGTTaa > 1:1166029/1‑69 (MQ=255)
tCTTGTAGTAATGGGTCACTCTTTTTTCTCGCTTTCTTCCTCTTCCGGCACCGGTTTGCTGGCGGTTaa < 1:2328165/69‑1 (MQ=255)
cTTGTAGTAATGGGTTACTCTTTTTTCTCGCTTTCTTCCTCTTCCGGCACCGGTTTGCTg > 1:1725424/1‑60 (MQ=255)
gtagtaATGGGTCACTCTTTTTTCTCGCTTTCTTCCTCTTCCGGCAc < 1:2971094/47‑1 (MQ=255)
gtagtaATGGGTCACTCTTTTTTCTCGCTTTCTTCCTCTTCCGGCACCGGTTTGCTGGCGGTTAACAgg < 1:1661730/69‑1 (MQ=255)
gtagtaACGGGTTACTCTTTTTTCTCGCTTTCTTCCTCTTCCGGCACCGGTTTGCTGGCGGTTAACAgg < 1:2597337/69‑1 (MQ=255)
tagtaATGGGTCACTCTTTTTTCTCGCTTTCTTCCTCTTCCGGCACCGGTTTGCTGGCGGTTAACAGGaa < 1:1901258/70‑1 (MQ=255)
tagtaATGGGTCACTCTTTTTTCTCGCTTTCTTCCTCTTCCGGCACCGGTTTGCTGGCGGTTAACAGGaa < 1:1305790/70‑1 (MQ=255)
gtaATGGGTCACTCTTTTTTCTCGCTTTCTTCCTCTTCCGGCACCGGTTTGCTGGCGGTTAACAGGAAggg < 1:2414113/71‑1 (MQ=255)
gtaATGGGTCACTCTTTTTTCTCGCTTTCTTCCTCTTCCGGCACCGGTTTGCTGGCGGTTAACAGGAAggg > 1:1350588/1‑71 (MQ=255)
aTGGGTCACTCTTTTTTCTCGCTTTCTTCCTCTTCCGGCACCGGTTTGCTGGCGGTTAACAGGAAGGGCg < 1:2678819/70‑1 (MQ=255)
aTGGGTCACTC‑TTTTTCTCGCTTTCTTCCTCTTCCGGCACCGGttt > 1:680571/1‑46 (MQ=39)
ggTCACTCTTTTTTCTCGCTTTCTTCCTCTTCCGGCACCGGt > 1:2113895/1‑42 (MQ=255)
ggTCACTCTTTTTTCTCGCTTTCTTCCTCTTCCGGCACCGGt > 1:3438080/1‑42 (MQ=255)
tCACTCTTTTTTCTCGCTTTCTTCCTCTTCCGGCACCGGTTTGCTGGCGGTTAACAGGAAGGGCGATtgct > 1:2614807/1‑71 (MQ=255)
tCACTCTTTTTTCTCGCTTTCTTCCTCTTCCGGCACCGGTTTGCTGGCGGTTAACAGGAAGGGCGATtgct < 1:1004709/71‑1 (MQ=255)
|
TCGTAAGAGTCAGAGATGAGCAGGCGTAATGTGGACATAACGATTTCCTTTCTTGTAGTAATGGGTCACTCTTTTTTCTCGCTTTCTTCCTCTTCCGGCACCGGTTTGCTGGCGGTTAACAGGAAGGGCGATTGCT > minE/2970370‑2970505
|
| 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
