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 F8 I0 R1
|
43 |
62.4 |
4721813 |
98.4% |
4646263 |
62.0 |
Breseq alignment
BRESEQ :: Evidence
|
| evidence |
seq id |
position |
mutation |
freq |
annotation |
gene |
description |
| RA |
W3110S.gb |
3,824,410 |
T→A |
100% |
pseudogene (543/687 nt) |
rph → |
ECK3633:JW3618:b3643; ribonuclease PH |
|
| |
seq id |
position |
ref |
new |
freq |
score (cons/poly) |
reads |
annotation |
genes |
product |
| * | W3110S.gb | 3,824,410 | 0 | T | A | 100.0%
| 239.1
/ NA
| 79 | pseudogene (543/687 nt) | rph | ECK3633:JW3618:b3643; ribonuclease PH |
| Reads supporting (aligned to +/- strand): ref base T (0/0); new base A (44/35); total (44/35) |
| Rejected as polymorphism: Frequency below/above cutoff threshold. |
| Rejected as polymorphism: Variant not supported by required number of reads on each strand. |
TAGCCGCAGTTTCTGTCGGAATTGTGAACGGCGAAGCGGTTTGCGATCTGGAATACGTTGAAGACTCTGCCGCAGAGACCGACATGAACGTAGTGATGACCGAAGACGGGCGCATCATTGAAGTGCAGGGGACGG > W3110S.gb/3824343‑3824477
|
tAGCCGCAGTTTCTGTCGGTATTGTAAACGGTGAAGCAATTTGCGATCTGGAATACGTTGAAGACTCAGcc > 1:2644508/1‑71 (MQ=255)
cGCAGTTTCTGTCGGTATTGTAAACGGTGAAGCAATTTGCGATCTGGAATACGTTGAAGACTCAGCCg > 1:2098201/1‑68 (MQ=255)
gCAGTTTCTGTCGGTATTGTAAACGGTGAAGCAATTTGCGATCTGGAATACGTTGAAGACTCAGCCGCaga < 1:2382290/71‑1 (MQ=255)
gCAGTTTCTGTCGGTATTGTAAACGGTGAAGCAATTTGCGATCTGGAATACGTTGAAGACTCAGCCGCaga < 1:4014277/71‑1 (MQ=255)
cAGTTTCTGTCGGTATTGTAAACGGTGAAGCAATTTGCGATCTGGAATACGTTGAAGACTCAGCCGCagag < 1:811571/71‑1 (MQ=255)
cAGTTTCTGTCGGTATTGTAAACGGTGAAGCAATTTGCGATCTGGAATACGTTGAAGACTCAGCCGCa > 1:3347983/1‑68 (MQ=255)
cAGTTTCTGTCGGTATTGTAAACGGTGAAGCAATTTGCGATCTGGAATACGTTGAAGACTCAGCCGCa > 1:1796857/1‑68 (MQ=255)
gTTTCTGTCGGTATTGTAAACGGTGAAGCAATTTGCGATCTGGAATACGTTGAAGACTCAGCCGCAGAGAc > 1:1708692/1‑71 (MQ=255)
ttCTGTCGGTATTGTAAACGGTGAAGCAATTTGCGATCTGGAATACGTTGAAGACTCAGCCGCAGAGAcc > 1:3281685/1‑70 (MQ=255)
ttCTGTCGGTATTGTAAACGGTGAAGCAATTTGCGATCTGGAATACGTTGAAGACTCAGCCGCAGAGAcc > 1:4556967/1‑70 (MQ=255)
tGTCGGTATTGTAAACGGTGAAGCAATTTGCGATCTGGAATACGTTGAAGACTCAGCCGCa < 1:749720/61‑1 (MQ=255)
ggtaTTGTAAACGGTGAAGCAATTTGCGATCTGGAATACGTTGAAGACTCAGCCGCAGAGACCGACATGaa > 1:2567568/4‑71 (MQ=255)
ggtaTTGTAAACGGTGAAGCAATTTGCGATCTGGAATACGTTGAAGACTCAGCCGCAGAGACCGACATGaa > 1:3605688/4‑71 (MQ=255)
gtaTTGTAAACGGTGAAGCAATTTGCGATCTGGAATACGTTGAAGACTCAGCCGc < 1:2546241/53‑1 (MQ=255)
gtaTTGTAAACGGTGAAGCAATTTGCGATCTGGAATACGTTGAAGACTCAGCCGCa > 1:451038/3‑56 (MQ=255)
gtaTTGTAAACGGTGAAGCAATTTGCGATCTGGAATACGTTGAAGACTCAGCCGCa > 1:1657567/3‑56 (MQ=255)
aTTGTAAACGGTGAAGCAATTTGCGATCTGGAATACGTTGAAGACTCAGCCGCAGAGACCGACAt > 1:299284/1‑65 (MQ=255)
ttGTAAACGGTGAAGCAATTTGCGATCTGGAATACGTTGAAGACTCAGCCg < 1:2915673/51‑1 (MQ=255)
ttGTAAACGGTGAAGCAATTTGCGATCTGGAATACGTTGAAGACTCAGCCGCa < 1:742734/53‑1 (MQ=255)
ttGTAAACGGTGAAGCAATTTGCGATCTGGAATACGTTGAAGACTCAGCCGCAGAGACCGACATGAACGt < 1:3199156/70‑1 (MQ=255)
gtaaaCGGTGAAGCAATTTGCGATCTGGAATACGTTGAAGACTCAGCCGCAGAGACCGACATGAACGTAGt > 1:2802439/4‑71 (MQ=255)
gtaaaCGGTGAAGCAATTTGCGATCTGGAATACGTTGAAGACTCAGCCGCAGAGACCGACATGAACGTAGt > 1:3588257/4‑71 (MQ=255)
gtaaaCGGTGAAGCAATTTGCGATCTGGAATACGTTGAAGACTCAGCCGCAGAGACCGACATGAACGTAGt > 1:755263/4‑71 (MQ=255)
aaaCGGTGAAGCAATTTGCGATCTGGAATACGTTGAAGACTCAGCCGCAGAGACCGACATGAACGTAGtga > 1:1728009/2‑71 (MQ=255)
aaCGGTGAAGCAATTTGCGATCTGGAATACGTTGAAGACTCAGCCGCAGAGACCGACATGAACGTAGtga < 1:4152279/70‑1 (MQ=255)
aCGGTGAAGCAATTTGCGATCTGGAATACGTTGAAGACTCAGCCGCAGAGACCGACATGAACGTAGtgat > 1:3651296/1‑70 (MQ=255)
aCGGTGAAGCAATTTGCGATCTGGAATACGTTGAAGACTCAGCCGCAGAGACCGACATGAACGTAGtgat > 1:613142/1‑70 (MQ=255)
aCGGTGAAGCAATTTGCGATCTGGAATACGTTGAAGACTCAGCCGCAGAGACCGACATGAACGTAGtgat > 1:976764/1‑70 (MQ=255)
ggtgAAGCAATTTGCGATCTGGAATACGTTGAAGACTCAGCCGCAGAGACCGACATGAACGTAGTGATGAc > 1:28994/4‑71 (MQ=255)
tgAAGCAATTTGCGATCTGGAATACGTTGAAGACTCAGCCGCAGAGACCGACATGAACGTAGTGATGACCg < 1:4042876/70‑1 (MQ=255)
tgAAGCAATTTGCGAGCTGGAATACGTTGAAGACTCAGCCGCAGAGACCGACATGAACGTAGTGATGAcc < 1:1028428/69‑1 (MQ=255)
atttGCGATCTGGAATACGTTGAAGACTCAGCCGCAGAGACCGACATGAACGTAGTGATGACCGAAGACgg < 1:2887232/70‑1 (MQ=255)
tttGCGATCTGGAATACGTTGAAGACTCAGCCGCAGAGACCGACATg < 1:2669996/47‑1 (MQ=255)
ttGCGATCTGGAATACGTTGAAGACTCAGCCGCAGAGACCGACATGAACGTAGTGATGACCGAAg < 1:49940/65‑1 (MQ=255)
tGCGATCTGGAATACGTTGAAGACTCAGCCGCAGGGACCGACATGAACGTAGTGATGACCGAAGACGGgcg > 1:1831695/1‑71 (MQ=255)
tGCGATCTGGAATACGTTGAAGACTCAGCCGCAGAGACCGACATGAACg > 1:1838411/1‑49 (MQ=255)
tGCGATCTGGAATACGTTGAAGACTCAGCCGCAGAGACCGACATGAACGTAGTGATGACCGAAGACGGgcg > 1:342337/1‑71 (MQ=255)
tGCGATCTGGAATACGTTGAAGACTCAGCCGCAGAGACCGACATGAACGTAGTGATGACCGAAGACGGgcg > 1:1060085/1‑71 (MQ=255)
gCGATCTGGAATACGTTGAAGACTCAGCCGCAGAGACCGACATGAACGTAGTGATGACCGAAGAc > 1:579942/1‑65 (MQ=255)
gCGATCTGGAATACGTTGAAGACTCAGCCGCAGAGACCGACATGAACGTAGTGATGACCGAAGAc > 1:4643574/1‑65 (MQ=255)
gCGATCTGGAATACGTTGAAGACTCAGCCGCAGAGACCGACATGAACGTAGTGATGACCGAAGAc > 1:4485929/1‑65 (MQ=255)
cGATCTGGAATACGTTGAAGACTCAGCCGCAGAGACCGACATGAACGTAGTGATGACCGAAGACGGgcgc < 1:3714237/70‑1 (MQ=255)
cGATCTGGAATACGTTGAAGACTCAGCCGCAGAGACCGACATGAACGTAGTGATGACCGAAGACGGGCGca > 1:150562/1‑71 (MQ=255)
gATCTGGAATACGTTGAAGACTCAGCCGCAGAGACCGACATGAACGTAGTGATGACCg < 1:789413/58‑1 (MQ=255)
tCTGGAATACGTTGAAGACTCAGCCGCAGAGACCGACATGa < 1:2718788/41‑1 (MQ=255)
cTGGAATACGTTGAAGACTCAGCCGCAGAGACCGACATGAACGTAGTGATGACCGAAGa > 1:1731779/1‑59 (MQ=255)
tGGAATACGTTGAAGACTCAGCCGCAGAGACCGACATGAACGTAGTGATGACCGaa < 1:4431881/56‑1 (MQ=255)
ggAATACGTTGAAGACTCAGCCGCAGAGACCGACATGAACGTAGTGATGACCGAAGACggg < 1:4526008/61‑1 (MQ=255)
gAATACGTTGAAGACTCAGCCGCAGAGACCGACATGAACGTAGTGATGACCGAAGACGGGCGcatc < 1:4691507/66‑1 (MQ=255)
gAATACGTTGAAGACTCAGCCGCAGAGACCGACATGAACGTAGTGATGACCGAAGACGGGCGcatc < 1:2504862/66‑1 (MQ=255)
gAATACGTTGAAGACTCAGCCGCAGAGACCGACATGAACGTAGTGATGACCGAAGACGGGCGCATCATTg < 1:4662667/70‑1 (MQ=255)
gAATACGTTGAAGACTCAGCCGCAGAGACCGACATGAACGTAGTGATGACCGAAGACGGGCGCATCATTg > 1:3084852/1‑70 (MQ=255)
gAATACGTTGAAGACTCAGCCGCAGAGACCGACATGAACGTAGTGATGACCGAAGACGGGCGCATCATTg < 1:3042439/70‑1 (MQ=255)
gAATACGTTGAAGACTCAGCCGCAGAGACCGACATGAACGTAGTGATGACCGAAGACGGGCGCATCATTg < 1:3037641/70‑1 (MQ=255)
aTACGTTGAAGACTCAGCCGCAGAGACCGACATGAACGTAGtgatg < 1:2462600/46‑1 (MQ=255)
tACGTTGAAGACTCAGCCGCAGAGACCGACATGAACGTAGtgatg < 1:1108314/45‑1 (MQ=255)
tACGTTGAAGACTCAGCCGCAGAGACCGACATGAACGTAGtgat < 1:4400110/44‑1 (MQ=255)
tACGTTGAAGACTCAGCCGCAGAGACCGACATGAACGTAGt < 1:332599/41‑1 (MQ=255)
cGTTGAAGACTCAGCCGCAGAGACCGACATGAACGTAGTGATGACCGAAGa > 1:766605/1‑51 (MQ=255)
cGTTGAAGACTCAGCCGCAGAGACCGACATGAACGTAGTGATGACCGAAGACggg > 1:1006139/1‑55 (MQ=255)
cGTTGAAGACTCAGCCGCAGAGACCGACATGAACGTAGTGATGACCGAAGACgg > 1:2858634/1‑54 (MQ=255)
cGTAGAAGACTCAGCCGCAGAGACCGACATGAACGTAGTGATGACCGAAGACgg > 1:2417557/1‑54 (MQ=255)
gTTGAAGACTCAGCCGCAGAGACCGACATGAACGTAGTGATGACCGAAGACGGGCGCATCATTGAAGTGCa < 1:1180680/71‑1 (MQ=255)
ttGAAGACTCAGCCGCAGAGACCGACATGAACGTAGtg < 1:4124459/38‑1 (MQ=255)
ttGAAGACTCAGCCGCAGAGACCGACATGAACGTAGTGATGACCGAAGACGGGCGCATCATTGAAGTGc < 1:3398475/69‑1 (MQ=255)
ttGAAGACTCAGCCGCAGAGACCGACATGAACGTAGTGATGACCGAAGACGGGCGCATCATTGAAGTGCa < 1:1744113/70‑1 (MQ=255)
tGAAGACTCAGCCGCAGAGACCGACATGAACGTAGTGATGAc > 1:3412790/1‑42 (MQ=255)
tGAAGACTCAGCCGCAGAGACCGACATGAACGTAGTGATGAc > 1:1153221/1‑42 (MQ=255)
tGAAGACTCAGCCGCAGAGACCGACATGAACGTAGTGATGAc > 1:3310827/1‑42 (MQ=255)
gAAGACTCAGCCGCAGAGACCGACATGAACGTAGtgat > 1:496411/1‑38 (MQ=255)
gAAGACTCAGCCGCAGAGACCGACATGAACGTAGTGATGACCGAAGa > 1:2255325/1‑47 (MQ=255)
gAAGACTCAGCCGCAGAGACCGACATGAACGTAGTGATGACCGAAGa > 1:4073670/1‑47 (MQ=255)
gAAGACTCAGCCGCAGAGACCGACATGAACGTAGTGATGACCGAAGACGGGCGCATCATTGAAGTGCAgtg > 1:2867330/1‑69 (MQ=255)
gAAGACTCAGCCGCAGAGACCGACATGAACGTAGTGATGACCGAAGACGGGCGCATCATTGAAGTGCAggg > 1:690108/1‑71 (MQ=255)
aaGACTCAGCCGCAGAGACCGACATGAACGTAGTGATGACCGAAGACGGGCGCATCATTGAAGTGCAggg < 1:3431418/70‑1 (MQ=255)
aGACTCAGCCGCAGAGACCGACATGAACGTAGTGATGACCGa < 1:4091960/42‑1 (MQ=255)
aGACTCAGCCGCAGAGACCGACATGAACGTAGTGATGACCGAAGACGGGCGCATCATTGAAGTGCAGGGGa > 1:2433863/1‑71 (MQ=255)
aGACTCAGCCGCAGAGACCGACATGAACGTAGTGATGACCGAAGACGGGCGCATCATTGAAGTGCAGGGGa < 1:2548499/71‑1 (MQ=255)
aCTCAGCCGCAGAGACCGACATGAACGTAGTGATGACCGaa > 1:723814/1‑41 (MQ=255)
ctcaGCCGCAGAGACCGACATGAACGTAGTGATGACCGAAGACGGGCGCATCATTGAAGTGCAGGGGACgg < 1:2799108/71‑1 (MQ=255)
|
TAGCCGCAGTTTCTGTCGGAATTGTGAACGGCGAAGCGGTTTGCGATCTGGAATACGTTGAAGACTCTGCCGCAGAGACCGACATGAACGTAGTGATGACCGAAGACGGGCGCATCATTGAAGTGCAGGGGACGG > W3110S.gb/3824343‑3824477
|
| Alignment Legend |
|---|
Aligned base mismatch/match (shaded by quality score): ATCG/ATCG < 3 ≤ ATCG/ATCG < 21 ≤ ATCG/ATCG < 32 ≤ ATCG/ATCG < 36 ≤ ATCG/ATCG |
Unaligned base: atcg Masked matching base: atcg Alignment gap: ‑ Deleted base: ‑ |
GATK/CNVnator alignment
N/A
