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 F17 I0 R2
|
276 |
45.3 |
3729697 |
93.0% |
3468618 |
60.6 |
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%
| 177.5
/ NA
| 60 | pseudogene (543/687 nt) | rph | ECK3633:JW3618:b3643; ribonuclease PH |
| Reads supporting (aligned to +/- strand): ref base T (0/0); new base A (32/28); total (32/28) |
| Rejected as polymorphism: Frequency below/above cutoff threshold. |
| Rejected as polymorphism: Variant not supported by required number of reads on each strand. |
GCAGTTTCTGTCGGAATTGTGAACGGCGAAGCGGTTTGCGATCTGGAATACGTTGAAGACTCTGCCGCAGAGACCGACATGAACGTAGTGATGACCGAAGACGGGCGCATCATTGAAGTGCAGGG > W3110S.gb/3824348‑3824472
|
gCAGTTTCTGTCGGTATTGTAAACGGTGAAGCAATTTGCGATCTGGAATACGTTGAAGACTCAGCCGCa < 1:525453/69‑1 (MQ=255)
ttCTGTCGGTATTGTAAACGGTGAAGCAATTTGCGATCTGGAATACGTTGAAGACTCAGCCGCagat < 1:885086/67‑2 (MQ=255)
ttCTGTCGGTATTGTAAACGGTGAAGCAATTTGCGATCTGGAATACGTTGAAGACTCAGCCGCagag < 1:2285045/67‑1 (MQ=255)
ttCTGTCGGTATTGTAAACGGTGAAGCAATTTGCGATCTGGAATACGTTGAAGACTCAGCCGCagag < 1:770426/67‑1 (MQ=255)
ttCTGTCGGTATTGTAAACGGTGAAGCAATTTGCGATCTGGAATACGTTGAAGACTCAGCCGCagag < 1:3194085/67‑1 (MQ=255)
ttCTGTCGGTATTGTAAACGGTGAAGCAATTTGCGATCTGGAATACGTTGAAGACTCAGCCGCagag < 1:2743509/67‑1 (MQ=255)
tCTGTCGGTATTGTAAACGGTGAAGCAATTTGCGATCTGGAATACGTTGAAGACTCAGcc > 1:1230306/1‑60 (MQ=255)
tCTGTCGGTATTGTAAACGGTGAAGCAATTTGCGATCTGGAATACGTTGAAGACTCAGcc > 1:1914151/1‑60 (MQ=255)
tCTGTCGGTATTGTAAACGGTGAAGCAATTTGCGATCTGGAATACGTTGAAGACTCAGcc > 1:55162/1‑60 (MQ=255)
tCTGTCGGTATTGTAAACGGTGAAGCAATTTGCGATCTGGAATACGTTGAAGACTCAGc < 1:2779168/59‑1 (MQ=255)
tCTGTCGGTATTGTAAACGGTGAAGCAATTTGCGATCTGGAATACGTTGAAGACTCAGc < 1:2080452/59‑1 (MQ=255)
ggtaTTGTAAACGGTGAAGCAATTTGCGATCTGGAATACGTTGAAGACTCAGCCGCAGAGACCGACATg < 1:629499/66‑1 (MQ=255)
taTTGTAAACGGTGAAGCAATTTGCGATCTGGAATACGTTGAAGACTCAGCCGCAGAGACCGACATGaa < 1:2159290/68‑1 (MQ=255)
aTTGTAAACGGTGAAGCAATTTGCGATCTGGAATACGTTGAAGACTCAGCCGCAGAGACCg > 1:153409/1‑61 (MQ=255)
aTTGTAAACGGTGAAGCAATTTGCGATCTGGAATACGTTGAAGACTCAGCCGCAGAGACCg > 1:1576728/1‑61 (MQ=255)
ttGTAAACGGTGAAGCAATTTGCGATCTGGAATACGTTGAAGACTCAGCCGCAGAGACCGACATGaa > 1:1524557/1‑67 (MQ=255)
ttGTAAACGGTGAAGCAATTTGCGATCTGGAATACGTTGAAGACTCAGCCGCAGAGACCGACATGaa > 1:3465008/1‑67 (MQ=255)
ttGTAAACGGTGAAGCAATTTGCGATCTGGAATACGTTGAAGACTCAGCCGCAGAGACCGACATGa > 1:3131117/1‑66 (MQ=255)
gtaaaCGGTGAAGCAATTTGCGATCTGGAATACGTTGAAGACTCAGCCGCAGAGACCGACATGAACGt < 1:1199541/65‑1 (MQ=255)
gtaaaCGGTGAAGCAATTTGCGATCTGGAATACGTTGAAGACTCAGCCGCAGAGACCGACATGAACGt > 1:336393/4‑68 (MQ=255)
taaaCGGTGAAGCAATTTGCGATCTGGAATACGTTGAAGACTCAGCCGCAGAGACCGACATGaa > 1:369341/3‑64 (MQ=255)
taaaCGGTGAAGCAATTTGCGATCTGGAATACGTTGAAGACTCAGCCGCAGAGACCGACATGaa > 1:657729/3‑64 (MQ=255)
taaaCGGTGAAGCAATTTGCGATCTGGAATACGTTGAAGACTCAGCCGCAGAGACCGACATGaa < 1:1097882/62‑1 (MQ=255)
taaaCGGTGAAGCAATTTGCGATCTGGAATACGTTGAAGACTCAGCCGCAGAGACCGACATGaa > 1:920554/3‑64 (MQ=255)
aaCGGTGAAGGAATTTGCGATCTGGAATACGTTGAAGACTCAGCCGCAGAGACCGACATGAACGTAGtg > 1:1949320/1‑69 (MQ=255)
aaCGGTGAAGCAATTTGCGATCTGGAATACGTTGAAGACTCAGCCGCAGAGACCGACATGAACGTAGtg > 1:1481256/1‑69 (MQ=255)
aaCGGTGAAGCAATTTGCGATCTGGAATACGTTGAAGACTCAGCCGCAGAGACCGACATGAACGTAGtg > 1:6194/1‑69 (MQ=255)
ggtgAAGCAATTTGCGATCTGGAATACGTTGAAGACTCAGCCGCAGAGACCGACATGAACGTAGtgatg < 1:1899764/66‑1 (MQ=255)
ggtgAAGCAATTTGCGATCTGGAATACGTTGAAGACTCAGCCGCAGAGACCGACATGAACGTAGtgatg < 1:3360150/66‑1 (MQ=255)
caatttGCGATCTGGAATACGTTGAAGACTCAGCCGCAGAGACCGACATGAAAGTAGTGATGACCGAAg > 1:2999652/4‑69 (MQ=255)
ttGCGATCTGGAATACGTTGAAGACTCAGCCGCAGAGACCGACATGAACGTAGTGATGACCGaa > 1:3380573/1‑64 (MQ=255)
ttGCGATCTGGAATACGTTGAAGACTCAGCCGCAGAGACCGACATGAACGTAGTGATGACCGaa > 1:2261091/1‑64 (MQ=255)
ttGCGATCTGGAATACGTTGAAGACTCAGCCGCAGAGACCGACATGAACGTAGTGATGACCGaa > 1:2422801/1‑64 (MQ=255)
ttGCGATCTGGAATACGTTGAAGACTCAGCCGCAGAGACCGACATGAACGTAGTGATGACCGaa > 1:2087958/1‑64 (MQ=255)
ttGCGATCTGGAATACGTTGAAGACTCAGCCGCAGAGACCGACATGAACGTAGTGATGACCGaa < 1:826539/64‑1 (MQ=255)
ttGCGATCTGGAATACGTTGAAGACTCAGCCGCAGAGACCGACATGAACGTAGTGATGACCGaa > 1:914524/1‑64 (MQ=255)
ttGCGATCTGGAATACGTTGAAGACTCAGCCGCAGAGACCGACATGAACGTAGTGATGACCGa > 1:2922922/1‑63 (MQ=255)
ttGCGATCTGGAATACGTTGAAGACTCAGCCGCAGAGACCGACATGAACGTAGTGATGACCGAAg < 1:3707515/65‑1 (MQ=255)
ttGCGATCTGGAATACGTTGAAGACTCAGCCGCAGAGACCGACATGAACGTAGTGATGACCGAAg < 1:1086864/65‑1 (MQ=255)
ttGCGATCTGGAATACGTTGAAGACTCAGCCGCAGAGACCGACATGAACGTAGTGATGACCGAAg < 1:939500/65‑1 (MQ=255)
tGCGATCTGGAATACGTTGAAGACTCAGCCGCAGAGAcc > 1:1246083/1‑39 (MQ=255)
tGCGATCTGGAATACGTTGAAGACTCAGCCGCAGAGACCGACATGAACGTAGTGATGACCGAAGACggg > 1:2280630/1‑69 (MQ=255)
tGCGATCTGGAATACGTTGAAGACTCAGCCGCAGAGACCGACATGAACGTAGTGATGACCGAAGACggg > 1:322165/1‑69 (MQ=255)
tGCGATCTGGAATACGTTGAAGACTCAGCCGCAGAGACCGACATGAACGTAGTGATGACCGAAGACggg > 1:2460102/1‑69 (MQ=255)
tGCGATCTGGAATACGTTGAAGACTCAGCCGCAGAGACCGACATGAACGTAGTGATGACCGAAGACggg > 1:3016228/1‑69 (MQ=255)
tGCGATCTGGAATACGTTGAAGACTCAGCCGCAGAGACCGAAATGAACGTAGTGATGACCGAAGACggg > 1:326525/1‑69 (MQ=255)
aTACGTTGAAGACTCAGCCGCAGAGACCGACATGAACGTAGTGATGACCGAAGACGGGCGcatc < 1:1060034/64‑1 (MQ=255)
aTACGTTGAAGACTCAGCCGCAGAGACCGACATGAACGTAGTGATGACCGAAGACGGGCGCATCATTg < 1:2590385/68‑1 (MQ=255)
aTACGTTGAAGACTCAGCCGCAGAGACCGACATGAACGTAGTGATGACCGAAGACGGGAGCATCATTg < 1:3687375/68‑1 (MQ=255)
cGTTGAAGACTCAGCCGCAGAGACCGACATGAACGTAGTGATGACCGAAGACGGGCGCATCATTGAAg > 1:1159536/1‑68 (MQ=255)
cGTTGAAGACTCAGCCGCAGAGACCGACATGAACGTAGTGATGACCGAAGACGGGCGCATCATTGAAg > 1:109673/1‑68 (MQ=255)
cGTTGAAGACTCAGCCGCAGAGACCGACATGAACGTAGTGATGACCGAAGACGGGCGCATCATTGAAg > 1:3501107/1‑68 (MQ=255)
ttGAAGACTCAGCCGCAGAGACCTACATGAACGTAGTGATGACCGAAGACGGGCGCATCATTGAAGTg < 1:3346275/68‑1 (MQ=255)
tGAAGACTCAGCCGCAGAGACCGACATGAACGTAGTGATGACCGAAGACGGGCGCATCATTGAAGTGCa > 1:3650746/1‑69 (MQ=255)
gAAGACTCAGCCGCAGAGACCGACATGAACGTAGTGATGACCGAAGACGGGCGCATCATTg < 1:607839/61‑1 (MQ=255)
gAAGACTCAGCCGCAGAGACCGACATGAACGTAGTGATGACCGAAGACGGGCGCATCATTg < 1:612171/61‑1 (MQ=255)
gAAGACTCAGCCGCAGAGACCGACATGAACGTAGTGATGACCGAAGACGGGCGCATCATTg < 1:2087527/61‑1 (MQ=255)
gAAGACTCAGCCGCAGAGACCGACATGAACGTAGTGATGACCGAAGACGGGCGCATCATTGa < 1:3141895/62‑1 (MQ=255)
gAAGACTCAGCCGCAGAGACCGACATGAACGTAGTGATGACCGAAGACGGGCGCATCATTGa < 1:1518912/62‑1 (MQ=255)
gACTCAGCCGCAGAGACCGACATGAACGTAGTGATGACCGAAGACGGGCGCATCATTGAAGTGCAggg < 1:724685/68‑1 (MQ=255)
|
GCAGTTTCTGTCGGAATTGTGAACGGCGAAGCGGTTTGCGATCTGGAATACGTTGAAGACTCTGCCGCAGAGACCGACATGAACGTAGTGATGACCGAAGACGGGCGCATCATTGAAGTGCAGGG > W3110S.gb/3824348‑3824472
|
| 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
