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 |
3,824,410 |
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 | 98.7%
| 214.4
/ ‑4.3
| 75 | pseudogene (543/687 nt) | rph | ECK3633:JW3618:b3643; ribonuclease PH |
| Reads supporting (aligned to +/- strand): ref base T (0/1); new base A (38/36); total (38/37) |
| Fisher's exact test for biased strand distribution p-value = 4.93e-01 |
| Kolmogorov-Smirnov test that lower quality scores support variant p-value = 9.82e-01 |
| Rejected as polymorphism: E-value score below prediction cutoff. |
| Rejected as polymorphism: Frequency below/above cutoff threshold. |
| Rejected as polymorphism: Variant not supported by required number of reads on each strand. |
GTAGCCGCAGTTTCTGTCGGAATTGTGAACGGCGAAGCGGTTTGCGATCTGGAATACGTTGAAGACTCTGCCGCAGAGACCGACATGAACGTAGTGATGACCGAAGACGGGCGCATCATTGAAGTGCAGGG > W3110S.gb/3824342‑3824472
|
gTAGCCGCAGTTTCTGTCGGTATTGTAAACGGTGAAGCAATTTGCGATCTGGAATACGTTGAAGACTCAGc > 1:630595/1‑71 (MQ=255)
cGCAGTTTCTGTCGGTATTGTAAACGGTGAAGCAATTTGCGATCTGGAATACGTTGAAGACTCAGCCg > 1:1853139/1‑68 (MQ=255)
ttCTGTCGGTATTGTAAACGGTGAAGCAATTTGCGATCTGGAATACGTTGAAGACTCAGCCGCAGAGAcc > 1:554003/1‑70 (MQ=255)
ttCTGTCGGTATTGTAAACGGTGAAGCAATTTGCGATCTGGAATACGTTGAAGACTCAGCCGCAGAGAcc > 1:225258/1‑70 (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)
ttGTAAACGGTGAAGCAATTTGCGATCTGGAATACGTTGAAGACTCAGCCGCAGAGACCGACATGAACg < 1:762581/69‑1 (MQ=255)
ttGTAAACGGTGAAGCAATTTGCGATCTGGAATACGTTGAAGACTCAGCCGCAGAGACCGACATGAACg < 1:2457143/69‑1 (MQ=255)
gtaaaCGGTGAAGCAATTTGCGATCTGGAATACGTTGAAGACTCAGCCGCAGAGACCGACATGAACGTa > 1:1168252/4‑69 (MQ=255)
gtaaaCGGTGAAGCAATTTGCGATCTGGAATACGTTGAAGACTCAGCCGCAGAGACCGACATGAACGTAGt > 1:276315/4‑71 (MQ=255)
gtaaaCGGTGAAGCAATTTGCGATCTGGAATACGTTGAAGACTCAGCCGCAGAGACCGACATGAACGTAGt > 1:3175103/4‑71 (MQ=255)
gtaaaCGGTGAAGCAATTTGCGATCTGGAATACGTTGAAGACTCAGCCGCAGAGACCGACATGAACGTAGt > 1:1240312/4‑71 (MQ=255)
gtaaaCGGTGAAGCAATTTGCGATCTGGAATACGTTGAAGACTCAGCCGCAGAGACCGACATGAACGTAGt > 1:1388081/4‑71 (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 < 1:907376/71‑1 (MQ=255)
aaCGGTGAAGCAATTTGCGATCTGGAATACGTTGAAGACTCAGCCGCAGAGACCGACATGAACGTAGtgat < 1:1130282/71‑1 (MQ=255)
gtgAAGCAATTTGCGATCTGGAATACGTTGAAGACTCAGCCGCAGAGACCGACATGa < 1:57526/55‑1 (MQ=255)
tgAAGCAATTTGCGATCTGGAATACGTTGAAGACTCAGCCGCa < 1:3128718/42‑1 (MQ=37)
tgAAGCAATTTGCGATCTGGAATACGTTGAAGACTCAGCCGCa < 1:506983/42‑1 (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)
aatttGCGATCTGGAATACGTTGAAGACTCAGCCGCAGAGACCGACATGAACGTAGTGATGACCGAAGACg > 1:298121/3‑71 (MQ=255)
tttGCGATCTGGAATACGTTGAAGACTCAGCCGCa < 1:3237565/35‑1 (MQ=255)
tttGCGATCTGGAATACGTTGAAGACTCAGCCGCAGAGACCGACATGAACGTAGtga > 1:3148883/1‑57 (MQ=255)
tttGCGATCTGGAATACGTTGAAGACTCAGCCGCAGAGACCGACATGAACGTAGtga > 1:362190/1‑57 (MQ=255)
tttGCGATCTGGAATACGTTGAAGACTCAGCCGCAGAGACCGACATGAACGTAGTGATGACCGaa < 1:15530/65‑1 (MQ=255)
tttGCGATCTGGAATACGTTGAAGACTCAGCCGCAGAGACCGACATGAACGTAGTGATGACCGAAGACggg > 1:1720791/1‑71 (MQ=255)
tGCGATCTGGAATACGTTGAAGACTCAGCCGCAGAGACCGACATGAACGt > 1:1721640/1‑50 (MQ=255)
tGCGATCTGGAATACGTTGAAGACTCAGCCGCAGAGACCGACATGAACGTAGtga > 1:1669028/1‑55 (MQ=255)
tGCGATCTGGAATACGTTGAAGACTCAGCCGCAGAGACCGACATGAACGTAGtga > 1:1793490/1‑55 (MQ=255)
tGCGATCTGGAATACGTTGAAGACTCAGCCGCAGAGACCGACATGAACGTAGtga > 1:901028/1‑55 (MQ=255)
tGCGATCTGGAATACGTTGAAGACTCAGCCGCAGAGACCGACATGAACGTAGtga > 1:467063/1‑55 (MQ=255)
tGCGATCTGGAATACGTTGAAGACTCAGCCGCAGAGACCGACATGAACGTAGtga > 1:2399681/1‑55 (MQ=255)
tGCGATCTGGAATACGTTGAAGACTCAGCCGCAGAGACCGACATGAACGTAGTGATGACCGAAGACGGgcg > 1:3746026/1‑71 (MQ=255)
gATCTGGAATACGTTGAAGACTCAGCCGCAGAGACCGACATGAACGt < 1:325975/47‑1 (MQ=255)
gATCTGGAATACGTTGAAGACTCAGCCGCAGAGACCGACATGAACGt < 1:2315496/47‑1 (MQ=255)
tCTGGAATACGTTGAAGACTCAGCCGCAGAGACCGACATGAACg < 1:39171/44‑1 (MQ=255)
tCTGGAATACGTTGAAGACTCAGCCGCAGAGACCGACATGAACg < 1:813733/44‑1 (MQ=255)
tCTGGAATACGTTGAAGACTCAGCCGCAGAGACCGACATGAACg < 1:2695107/44‑1 (MQ=255)
tCTGGAATACGTTGAAGACTCAGCCGCAGAGACCGACATGAACg < 1:2408848/44‑1 (MQ=255)
tCTGGAATACGTTGAAGACTCAGCCGCAGAGACCGACATGAACGTAGTGATGACCGaa < 1:2197058/58‑1 (MQ=255)
cTGGAATACGTTGAAGACTCAGCCGCAGAGACCGACATGAACGTAGTGATGACCGAAGACGGGCGcatcat > 1:1030242/1‑71 (MQ=255)
tGGAATACGTTGAAGACTCAGCCGCAGAGACCGACATGAACGTa > 1:897119/1‑44 (MQ=255)
tGGAATACGTTGAAGACTCAGCCGCAGAGACCGACATGAACGTAGTGATGACCGaa < 1:3095719/56‑1 (MQ=255)
tgAATAGGTTGAAGACTCAGCCGCAGAGACCGACATGAACGt < 1:3336341/41‑1 (MQ=255)
ggAATACGTTGAAGACTCAGCCGCAGAGACCGACATGAACGTAGtgatga > 1:910964/1‑50 (MQ=255)
gAATATGTTGAAGACTCTGCCGCAGAGACCGACATGAACGTAGTGATGACCGAAGACGGGCGtatca < 1:3701801/67‑1 (MQ=255)
gAATACGTTGAAGACTCAGCCGCAGAGACCGACATGAACGTAGtga > 1:1818529/1‑46 (MQ=255)
gAATACGTTGAAGACTCAGCCGCAGAGACCGACATGAACGTAGtga > 1:3126387/1‑46 (MQ=255)
gAATACGTTGAAGACTCAGCCGCAGAGACCGACATGAACGTAGTGATGACCGAAGACGGGCGcatc < 1:3205387/66‑1 (MQ=255)
gAATACGTTGAAGACTCAGCCGCAGAGACCGACATGAACGTAGTGATGACCGAAGACGGGCGCATCATTg > 1:3632285/1‑70 (MQ=255)
aaTACGTTGAAGACTCAGCCGCAGAGACCGACATGAACGTAGTGATGACCGAAGACGGGCGCATCATTg > 1:18727/1‑69 (MQ=255)
tACGTTGAAGACTCAGCCGCAGAGACCGACATGAACGTAGTGATGACCGaa < 1:1207571/51‑1 (MQ=255)
tACGTTGAAGACTCAGCCGCAGAGACCGACATGAACGTAGTGATGACCGa < 1:3492460/50‑1 (MQ=255)
tACGTTGAAGACTCAGCCGCAGAGACCGACATGAACGTAGTGATGACCGa < 1:2977033/50‑1 (MQ=255)
aCGTTGAAGACTCAGCCGCAGAGACCGACATGAACGTAGTGATGACCGa < 1:230477/49‑1 (MQ=255)
cGTTGAAGACTCAGCCGCAGAGACCGACATGAACGTAGTGATGACCGAAGACGGGCGCATCATTGAAGTg < 1:1771647/70‑1 (MQ=255)
cGTTGAAGACTCAGCCGCAGAGACCGACATGAACGTAGTGATGACCGAAGACGGGCGCATCATTGAAGTg > 1:2074081/1‑70 (MQ=255)
cGTTGAAGACTCAGCCGCAGAGACCGACATGAACGTAGTGATGACCGAAGACGGGCGCATCATTGAAGTg < 1:2147715/70‑1 (MQ=255)
cGTTGAAGACTCAGCCGCAGAGACCGACATGAACGTAGTGATGACCGAAGACGGGCGCATCATTGAAGTGc < 1:1350181/71‑1 (MQ=255)
cGTTGAAGACTCAGCCGCAGAGACCGACATAAACGTAGTGATGACCGaa > 1:2991675/1‑49 (MQ=255)
cGTTGAAGACTCAGCCGCAGAGACCGACATAAACGTAGTGATGACCGaa > 1:1349197/1‑49 (MQ=255)
cGTTGAAGACTCAGCCGCAGAGACCGACATAAACGTAGTGATGACCGaa > 1:3230523/1‑49 (MQ=255)
gTTGAAGACTCAGCCGCAGAGACCGACATGAACGTAGTGATGACCGAAGACGGGCGCATCATTGAAGTGCa < 1:3715704/71‑1 (MQ=255)
gAAGACTCAGCCGCAGAGACCGACATGAACGTAGTGATGACCGAAGACGGGCGCATCATTGAAGTGCAggg > 1:2123540/1‑71 (MQ=255)
aCTCAGCCGCAGAGACCGACATGAACGTAGtgatg > 1:2736285/1‑35 (MQ=255)
aCTCAGCCGCAGAGACCGACATGAACGTAGTGATGACCGAAGACGGGCGcatca > 1:3418304/1‑54 (MQ=255)
|
GTAGCCGCAGTTTCTGTCGGAATTGTGAACGGCGAAGCGGTTTGCGATCTGGAATACGTTGAAGACTCTGCCGCAGAGACCGACATGAACGTAGTGATGACCGAAGACGGGCGCATCATTGAAGTGCAGGG > W3110S.gb/3824342‑3824472
|
| 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
