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 |
|
A1 F1 I0 R2
|
532 |
47.8 |
3863072 |
94.9% |
3666055 |
61.4 |
Breseq alignment
BRESEQ :: Evidence
|
| evidence |
seq id |
position |
mutation |
freq |
annotation |
gene |
description |
| RA |
W3110S.gb |
3,824,380 |
2 bp→AA |
100% |
pseudogene (513‑514/687 nt) |
rph → |
ECK3633:JW3618:b3643; ribonuclease PH |
|
| |
seq id |
position |
ref |
new |
freq |
score (cons/poly) |
reads |
annotation |
genes |
product |
| * | W3110S.gb | 3,824,380 | 0 | G | A | 100.0%
| 184.8
/ NA
| 65 | pseudogene (513/687 nt) | rph | ECK3633:JW3618:b3643; ribonuclease PH |
| Reads supporting (aligned to +/- strand): ref base G (0/0); new base A (29/36); total (29/36) |
| Rejected as polymorphism: Frequency below/above cutoff threshold. |
| Rejected as polymorphism: Variant not supported by required number of reads on each strand. |
| * | W3110S.gb | 3,824,381 | 0 | G | A | 100.0%
| 185.0
/ NA
| 65 | pseudogene (514/687 nt) | rph | ECK3633:JW3618:b3643; ribonuclease PH |
| Reads supporting (aligned to +/- strand): ref base G (0/0); new base A (29/36); total (29/36) |
| Rejected as polymorphism: Frequency below/above cutoff threshold. |
| Rejected as polymorphism: Variant not supported by required number of reads on each strand. |
TGAAAACCAATCCGATGAAAGGGATGGTAGCCGCAGTTTCTGTCGGAATTGTGAACGGCGAAGCGGTTTGCGATCTGGAATACGTTGAAGACTCTGCCGCAGAGACCGACATGAACGTAGTGATGACCG > W3110S.gb/3824316‑3824444
||
tGAAAACCAACCCGATGAAAGGGATGGTAGCCGCAGTTTCTGTCGGTATTGTAAACGGTGAAGCAATTTGc > 1:3640684/1‑71 (MQ=255)
gAAAACCAACCCGATGAAAGGGATGGTAGCCGCAGTTTCTGTCGGTATTGTAAACGGTGAAGCAATTTGc > 1:1784038/1‑70 (MQ=255)
aaaaCCAACCCGATGAAAGGGATGGTAGCCGCAGTTTCTGTCGGTATTGTAAACGGTGAAGCAATTTGCg < 1:2658297/70‑1 (MQ=255)
aaaaCCAACCCGATGAAAGGGATGGTAGCCGCAGTTTCTGTCGGTATTGTAAACGGTGAAGCAATTTGCGa > 1:249979/1‑71 (MQ=255)
aaaCCAACCCGATGAAAGGGATGGTAGCCGCAGTTTCTGTCGGTATTGTAAACGGTGAAGCAATTTGCGAt > 1:650640/1‑71 (MQ=255)
aaccaaccCGATGAAAGGGATGGTAGCCGCAGTTTCTGTCGGTATTGTAAACGGTGAAGCAATTTGc > 1:3282768/1‑67 (MQ=255)
aCCAACCCGATGAAAGGGATGGTAGCCGCAGTTTCTGTCGGTATTGTAAACGGTGAAGCAATTTGCGATCt > 1:583756/1‑71 (MQ=255)
cAACCCGATGAAAGGGATGGTAGCCGCAGTTTCTGTCGGTATTGTAAACGGTGAAGCAATTTGCGATCTg > 1:1385818/1‑70 (MQ=255)
acccGATGAAAGGGATGGTAGCCGCAGTTTCTGTCGGTATTGTAAACGGTGAAGCAATTTGCGATCTGGaa < 1:1293884/69‑1 (MQ=255)
aTGAAAGGGATGGTAGCCGCAGTTTCTGTCGGTATTGTAAACGGTGAAGCAATTTGCGa < 1:1270416/59‑1 (MQ=255)
gAAAGGGATGGTAGCCGCAGTTTCTGTCGGTATTGTAAACGGTGAATCAATTTGCGa > 1:1381513/1‑57 (MQ=255)
aaGGGATTGTAGCCGCAGTTTCTGTCGGTATTGTAAACGGTGAAGCAATTTGCGATCTGGAATACGTTGaa < 1:2974998/71‑1 (MQ=255)
aGGGATGGTAGCCGCAGTTTCTGTCGGTATTGTAAACGGTGAAGCAATTTGCGATCTGGAATACGTTg > 1:3555599/1‑68 (MQ=255)
gATGGTAGCCGCAGTTTCTGTCGGTATTGTAAACGGTGAAGCAATTTGCGATCTGGAATACGTTGAAGAct < 1:1559881/71‑1 (MQ=255)
tGGTAGCCGCAGTTTCTGTCTGTATTGTAAACGGTGAAGCAATTTGCGATCTGGAATACGTTg < 1:2940540/63‑1 (MQ=255)
tGGTAGCCGCAGTTTCTGTCGGTATTGTAAACGGTGAAGCAATTTGCGATCTgg < 1:1247329/54‑1 (MQ=255)
tGGTAGCCGCAGTTTCTGTCGGTATTGTAAACGGTGAAGCAATTTGCGATCTgg < 1:1253981/54‑1 (MQ=255)
tGGTAGCCGCAGTTTCTGTCGGTATTGTAAACGGTGAAGCAATTTGCGATCTGGAATACGTTg < 1:1212511/63‑1 (MQ=255)
tGGTAGCCGCAGTTTCTGTCGGTATTGTAAACGGTGAAGCAATTTGCGATCTGGAATACGTTg < 1:3700645/63‑1 (MQ=255)
tGGTAGCCGCAGTTTCTGTCGGTATTGTAAACGGTGAAGCAATTTGCGATCTGGAATACGTTg < 1:2170792/63‑1 (MQ=255)
tGGTAGCCGCAGTTTCTGTCGGTATTGTAAACGGTGAAGCAATTTGCGATCTGGAATACGTTGaa < 1:1081231/65‑1 (MQ=255)
tGGTAGCCGCAGTTTCTGTCGGTATTGTAAACGGTGAAGCAATTTGCGATCTGGAATACGTTGAAGAct > 1:131747/1‑69 (MQ=255)
tGGTAGCCGCAGTTTCTGTCGGTATTGTAAACGGTGAAGCAATTTGCGATCTGGAATACGTTGAAGAct > 1:651598/1‑69 (MQ=255)
tGGTAGCCGCAGTTTCTGTCGGTATTGTAAACGGTGAAGCAATTTGCGATCTGGAATACGTTGAAGAct > 1:518440/1‑69 (MQ=255)
ggTAGCCGCAGTTTCTGTCGGTATTGTAAACGGTGAAGCAATTTGCGATCTGGAATACGTTGAAGActc < 1:3609772/69‑1 (MQ=255)
ggTAGCCGCAGTTTCTGTCGGTATTGTAAACGGTGAAGCAATTTGCGATCTGGAATACGTTGAAGActc < 1:3636939/69‑1 (MQ=255)
gTAGCCGCAGTTTCTGTCGGTATTGTAAACGGTGAAGCAATTTGCGATCTGGAATACGTTGAAGACTCAGc > 1:630595/1‑71 (MQ=255)
gCCGCAGTTTCTGTCGGTATTGTAAACGGTGAAGCAATTTGc > 1:2512161/1‑42 (MQ=19)
cGCAGTTTCTGTCGGTATTGTAAACGGTGAAGCAATTTGCGATCTGGAATACGTTGAAGACTCAGCCg > 1:1853139/1‑68 (MQ=255)
ttCTGTCGGTATTGTAAACGGTGAAGCAATTTGCGATCTGGAATACGTTGaa > 1:3583759/1‑52 (MQ=255)
ttCTGTCGGTATTGTAAACGGTGAAGCAATTTGCGATCTGGAATACGTTGAAGACTCAGCCGCAGAGAcc > 1:225258/1‑70 (MQ=255)
ttCTGTCGGTATTGTAAACGGTGAAGCAATTTGCGATCTGGAATACGTTGAAGACTCAGCCGCAGAGAcc > 1:554003/1‑70 (MQ=255)
tCTGTCGGTATTGTAAACGGTGAAGCAATTTGCGATCTGGAATACGTTGaa > 1:1870366/1‑51 (MQ=255)
tCTGTCGGTATTGTAAACGGTGAAGCAATTTGCGATCTGGAATACGTTGAAGACTCAGCCGCa > 1:3279704/1‑63 (MQ=255)
tCTGTCGGTATTGTAAACGGTGAAGCAATTTGCGATCTGGAATACGTTGAAGACTCAGCCGCAGAGACCg < 1:3199485/70‑1 (MQ=255)
tCTGTCGGTATTGTAAACGGTGAAGCAATTTGCGATCTGGAATACGTTGAAGACTCAGCCGCAGAGACCGa > 1:1063349/1‑71 (MQ=255)
tCGGTATTGTAAACGGTGAAGCAATTTGCGATCTGGAATACGTTGAAGACTCAGCCGCAGAGACCGACATg < 1:2718677/71‑1 (MQ=255)
ggtaTTGTAAACGGTGAAGCAATTTGCGATCTGGAATACGTTGAAGACTCAGCCGCAGAGACCGACATGaa < 1:3193241/68‑1 (MQ=255)
aTTGTAAACGGTGAAGCAATTTGCGATCTGGAATACGTTGaa > 1:1198428/1‑42 (MQ=25)
ttGTAAACGGTGAAGCAATTTGCGATCTGGAATACg < 1:2736220/36‑1 (MQ=16)
ttGTAAACGGTGAAGCAATTTGCGATCTGGAATACg < 1:669687/36‑1 (MQ=16)
ttGTAAACGGTGAAGCAATTTGCGATCTGGAATACg < 1:2845961/36‑1 (MQ=16)
ttGTAAACGGTGAAGCAATTTGCGATCTGGAATACGTTGaa < 1:3810711/41‑1 (MQ=25)
ttGTAAACGGTGAAGCAATTTGCGATCTGGAATACGTTGa < 1:3037496/40‑1 (MQ=25)
ttGTAAACGGTGAAGCAATTTGCGATCTGGAATACGTTGAAGACTCAGCCGCAGAGACCGACATGAACg < 1:762581/69‑1 (MQ=255)
ttGTAAACGGTGAAGCAATTTGCGATCTGGAATACGTTGAAGACTCAGCCGCAGAGACCGACATGAACg < 1:2457143/69‑1 (MQ=255)
tgtaAACGGTGAAGCAATTTGCGATCTGGAATACGTTGa < 1:3401806/39‑1 (MQ=21)
gtaaaCGGTGAAGCAATTTGCGATCTGGAATACGTTGAAGACTCAGCCGCAGAGACCGACATGAACGTa > 1:1168252/4‑69 (MQ=255)
gtaaaCGGTGAAGCAATTTGCGATCTGGAATACGTTGAAGACTCAGCCGCAGAGACCGACATGAACGTAGt > 1:1388081/4‑71 (MQ=255)
gtaaaCGGTGAAGCAATTTGCGATCTGGAATACGTTGAAGACTCAGCCGCAGAGACCGACATGAACGTAGt > 1:1240312/4‑71 (MQ=255)
gtaaaCGGTGAAGCAATTTGCGATCTGGAATACGTTGAAGACTCAGCCGCAGAGACCGACATGAACGTAGt > 1:3175103/4‑71 (MQ=255)
gtaaaCGGTGAAGCAATTTGCGATCTGGAATACGTTGAAGACTCAGCCGCAGAGACCGACATGAACGTAGt > 1:276315/4‑71 (MQ=255)
gtaaaCGGTGAAGCAATTTGCGATCTGGAATACGTTGAAGACTAAGCCGCAGAGACCGACATGAACGTAGt > 1:1776242/4‑71 (MQ=255)
gtaaaCGGTGAAGCAATTTGCGATCTGGAATAAGTTGAAGACTCAGCCGCAGAGACCGACATGAACGTa > 1:1183083/4‑69 (MQ=255)
taaaCGGTGAAGCAATTTGCGATCTGGAATACGTTGAAGACTCAGCCGCAGAGACCGACATGAACGTAGt < 1:1857207/68‑1 (MQ=255)
aaaCGGTGAACCAATTTGCGATCTGGAATACGTTGAAGACTCAGCCGCAGAGACCGACATGAACGTAGtg < 1:1078379/69‑1 (MQ=255)
aaCGGTGAAGCAATTTGCGATCTGGAATACGTTGAAGACTCAGCCGCAGAGACCGACATGAACGTAGtgat < 1:1130282/71‑1 (MQ=255)
aaCGGTGAAGCAATTTGCGATCTGGAATACGTTGAAGACTCAGCCGCAGAGACCGACATGAACGTAGtgat < 1:907376/71‑1 (MQ=255)
gtgAAGCAATTTGCGATCTGGAATACGTTGAAGACTCAGCCGCAGAGACCGACATGa < 1:57526/55‑1 (MQ=255)
tgAAGCAATTTGCGATCTGGAATACGTTGAAGACTCAGCCGCa < 1:506983/42‑1 (MQ=37)
tgAAGCAATTTGCGATCTGGAATACGTTGAAGACTCAGCCGCa < 1:3128718/42‑1 (MQ=37)
tgAAGCAATTTGCGATCTGGAATACGTTGAAGACTCAGCCGCa < 1:2702629/42‑1 (MQ=37)
tgAAGCAATTTGCGATCTGGAATACGTTGAAGACTCAGCCGCAGAGACCGACATGAACGTAGTGATGACCg < 1:330253/70‑1 (MQ=255)
gAAGCAATTTGCGATCTGGAATACGTTGAAGACTCAGCCGCAGAGACCGACATGaa < 1:2556700/56‑1 (MQ=255)
gAAGCAATTTGCGATCTGGAATACGTTGAAGACTCAGCCGCAGAGACCGACATGaa < 1:879190/56‑1 (MQ=255)
||
TGAAAACCAATCCGATGAAAGGGATGGTAGCCGCAGTTTCTGTCGGAATTGTGAACGGCGAAGCGGTTTGCGATCTGGAATACGTTGAAGACTCTGCCGCAGAGACCGACATGAACGTAGTGATGACCG > W3110S.gb/3824316‑3824444
|
| 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
