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 |
832,712 |
T→G |
8.7% |
S390S (TCT→TCG) |
narG → |
nitrate reductase 1, alpha subunit |
|
| |
seq id |
position |
ref |
new |
freq |
score (cons/poly) |
reads |
annotation |
genes |
product |
| * | minE | 832,712 | 0 | T | G | 8.7%
| 109.8
/ 4.5
| 46 | S390S (TCT→TCG) | narG | nitrate reductase 1, alpha subunit |
| Reads supporting (aligned to +/- strand): ref base T (22/20); new base G (2/2); total (24/22) |
| Fisher's exact test for biased strand distribution p-value = 1.00e+00 |
| Kolmogorov-Smirnov test that lower quality scores support variant p-value = 9.84e-01 |
GAAAACAATCCGGAATGGAAAACTGTCGCCTTTAATACCAATGGCGAAATGGTTGCGCCGAACGGTTCTATTGGCTTCCGCTGGGGCGAGAAGGGCAAATGGAATCTTGAGCAGCGCGACGGCAAAACTGGCGAAGA > minE/832644‑832780
|
gAAAACAATCCGGAATGGAAAACTGTCGCCTTTAATACCAATGGCGAAATGGTTGCGCCGAACGGTTCTAt > 1:3845632/1‑71 (MQ=255)
agcaaCAATCCGCAGTGGAAAACCGTAGCAGTTAATACCGCAGGTGAATTGGTAGTGCCGAACGGTTCGAt < 1:1198656/68‑1 (MQ=255)
aaaCAATCCGGAATGGAAAACTGTCGCCTTTAATACCAATGGCGAAATGGTTGCGCCGAACGGTTCTATTg > 1:1945875/1‑71 (MQ=255)
aaCAATCCGGAATGGAAAACTGTCGCCTTTAATACCAATGGCGAAATGGTTGCGCCGAACGGTTCTATTgg < 1:1870889/71‑1 (MQ=255)
aCAATCCGGAATGGAAAACTGTCGCCTTTAATACCAATGGCGAAATGGTTGCGCCGAACGGTTCTATTGGc > 1:690940/1‑71 (MQ=255)
aaTCCGGAATGGAAAACTGTCGCCTTTAATACCAATGGCGAAATGGTTGCGCCGAACGGTTCTATTGGCtt < 1:939188/71‑1 (MQ=255)
aaTCCGGAATGGAAAACTGTCGCCTTTAATACCAATGGCGAAATGGTTGCGCCGAACGGTTCTATTGGCt < 1:694246/70‑1 (MQ=255)
aaTCCGCAGTGGAAAACCGTAGCAGTTAATACCGCAGGTGAATTGGTAGTGCCGAACGGTTCGATTGGttt > 1:63254/1‑71 (MQ=255)
ccGGAATGGAAAACTGTCGCCTTTAATACCAATGGCGAAATGGTTGCGCCGAACGGTTCTATTGGCTTCCg > 1:398101/1‑71 (MQ=255)
gAATGGAAAACTGTCGCCTTTAATACCAATGGCGAAATGGTTGCGCCGAACGGTTCTATTGGCTTCCGCTg < 1:3497072/71‑1 (MQ=255)
gAATGGAAAACTGTCGCCTTTAATACCAATGGCGAAATGGTTGCGCCGAACGGTTCTATTGGCTTCCGCTg > 1:3505311/1‑71 (MQ=255)
gAATGGAAAACTGTCGCCTTTAATACCAATGGCGAAATGGTTGCGCCGAACGGTTCTATTGGCTTCCGCTg < 1:320852/71‑1 (MQ=255)
gAATGGAAAACTGTCGCCTTTAATACCAATGGCGAAATGGTTGCGCCGAACGGTTCTATTGGCTTCCGCTg > 1:64398/1‑71 (MQ=255)
gtGGAAAACCGTAGCAGTTAATACCGCAGGTGAATTGGTAGTGCCGAACGGTTCGATTGGTTTCCGCTggg < 1:699230/70‑1 (MQ=255)
tGGAAAACTGTCGCCTTTAATACCAATGGCGAAATGGTTGCGCCGAACGGTTCt < 1:2806182/54‑1 (MQ=255)
tGGAAAACTGTCGCCTTTAATACCAATGGCGAAATGGTTGCGCCGAACGGTTCt < 1:670058/54‑1 (MQ=255)
aaaaCTGTCGCCTTTAATACCAATGGCGAAATGGTTGCGCCGAACGGTTCTATTGGCTTCCGCTg > 1:2195524/1‑65 (MQ=255)
aaaCTGTCGCCTTTAATACCAATGGCGAAATGGTTGCGCCGAACGGTTCTATTGGCTTCCGCTg < 1:3455641/64‑1 (MQ=255)
aaCTGTCGCCTTTAATACCAATGGCGAAATGGTTGCGCCGAACGGTTCTATTGGCTTCCGCTGGGGCgaga < 1:3220860/71‑1 (MQ=255)
aCTGTCGCCTTTAATACCAATGGCGAAATGGTTGCGCCGAACGGTTCTATTGGCTTCCGCTGGGGCGAGaa < 1:308044/71‑1 (MQ=255)
cTTTAATACCAATGGCGAAATGGTTGCGCCGAACGGTTCTATTGGCTTCCGCTGGGGCGAGAAGGGCAAAt > 1:1104260/1‑71 (MQ=255)
tttAATACCAATGGCGAAATGGTTGCGCCGAACGGTTCTATTGGCTTCCGCTGGGGCGAGAAggg > 1:3295014/1‑65 (MQ=255)
tttAATACCAATGGCGAAATGGTTGCGCCGAACGGTTCTATTGGCTTCCGCTGGGGCGAGAAgg > 1:959610/1‑64 (MQ=255)
tAATACCAATGGCGAAATGGTTGCGCCGAACGGTTCTATTGGCTTCCGCTGGGGCGAGAAGGGCAAATgg < 1:1235800/70‑1 (MQ=255)
aaTACCAATGGCGAAATGGTTGCGCCGAACGGTTCTATTGGCTTCCGCTGGGGCGAGAAGGGCAAATGGaa > 1:783362/1‑71 (MQ=255)
tACCAATGGCGAAATGGTTGCGCCGAACGGTTCTATTGGCTTCCGCTggg > 1:3758320/1‑50 (MQ=255)
aCCAATGGCGAAATGGTTGCGCCGAACGGTTCTATTGCCTTCCGCTGGGGCGAGAAGGGCa < 1:757441/61‑1 (MQ=255)
tGGCGAAATGGTTGCGCCGAACGGTTCTATTGGCTTCCGCTggg < 1:3951377/44‑1 (MQ=255)
tGGCGAAATGGTTGCGCCGAACGGTTCTATTGGCTTCCGCTGGGGCGAGAAGGGCAAATGGAATCTTGagc < 1:558955/71‑1 (MQ=255)
gCGAAATGGTTGCGCCGAACGGTTCTATTGGCTTCCGCTGGGGCGAGAAGGTCAAATGGAATCTTGagcag > 1:3361745/1‑71 (MQ=255)
gCGAAATGGTTGCGCCGAACGGTTCTATTGGCTTCCGCTGGGGCGAGAAGGGCAAATGGAATCTTGagcag > 1:3840418/1‑71 (MQ=255)
gCGAAATGGTTGCGCCGAACGGTTCTATTGGCTTCCGCTGGGGCGAGAAGGGCAAATGGAATCTTGagcag > 1:1921927/1‑71 (MQ=255)
gCGAAATGGTTGCGCCGAACGGTTCTATTGGCTTCCGCTGGGGCGAGAAGGGCAAATGGAATCTTGagca < 1:683252/70‑1 (MQ=255)
gAAATGGTTGCGCCGAACGGTTCTATTGGCTTCCGCTGGGGCGAGAAGGGCa < 1:1670657/52‑1 (MQ=255)
gAAATGGTTGCGCCGAACGGTTCTATTGGCTTCCGCTGGGGCGAGAAGGGCAAATGGAATCTTg < 1:3736617/64‑1 (MQ=255)
aaTGGTTGCGCCGAACGGTTCTATTGGCTTCCGCTGGGGCGAGAAGGGCAAATGGAATCTTGAGCAgcgc > 1:431527/1‑70 (MQ=255)
tGGTTGCGCCGAACGGTTCTATTGGCTTCCGCTGGGGCGAGAAGGGCAAATGGAATCTTGAGCAGCGCGAc > 1:2860741/1‑71 (MQ=255)
tGGTTGCGCCGAACGGTTCTATTGGCTTCCGCTGGGGCGAGAAGGGCAAATGGAATCTTGAGCAGCGCGAc < 1:3678742/71‑1 (MQ=255)
ggTTGCGCCGAACGGTTCTATTGGCTTCCGCTGGGGCGAGAAGGGCAAATGGAATCTTGAGCAGCGCGa < 1:3177440/69‑1 (MQ=255)
gtgcCGAACGGTTCGATTGGTTTCCGCTGGGGAGAAAAAGGCAAATGGaa > 1:3104719/3‑50 (MQ=25)
aaCGGTTCTATTGGCTTCCGCTGGGGCGAGAAGGGCAAATGGAATCTTGAGCAGCGCGACGGCAAAACTgg > 1:1963597/1‑71 (MQ=255)
aaCGGTTCTATTGGCTTCCGCTGGGGCGAGAAGGGCAAATGGAATCTTGAGCAGCGCGACGGCAAAACTg > 1:3528698/1‑70 (MQ=255)
aCGGTTCTATTGGCTTCCGCTGGGGCGAGAAGGGCAAATGGAATCTTg > 1:3896115/1‑48 (MQ=255)
ggTTCTATTGGCTTCCGCTGGGGCGAGAAGGGCAAATGGAATCTTGAGCAGCGCGACGGCAAAACTGGCga < 1:1908242/71‑1 (MQ=255)
gTTCTATTGGCTTCCGCTGGGGCGAGAAGGGCAAATGGAATCTTGAGCAGCGCGACGGCAAAACTGGCg > 1:3730915/1‑69 (MQ=255)
cTATTGGCTTCCGCTGGGGCGAGAAGGGCAAATGGAATCTTGAGCAGCGCGACGGCAAAACTGGCgaaga > 1:3148223/1‑70 (MQ=255)
cTATTGGCTTCCGCTGGGGCGAGAAGGGCAAATGGAATCTTGAGCAGCGCGACGGCAAAACTGGCgaaga < 1:1464670/70‑1 (MQ=255)
cTATTGGCTTCCGCTGGGGCGAGAAGGGCAAATGGAATCTTGAGCAGAGCGACGGCAAAACTGGCgaaga < 1:3844998/70‑1 (MQ=255)
|
GAAAACAATCCGGAATGGAAAACTGTCGCCTTTAATACCAATGGCGAAATGGTTGCGCCGAACGGTTCTATTGGCTTCCGCTGGGGCGAGAAGGGCAAATGGAATCTTGAGCAGCGCGACGGCAAAACTGGCGAAGA > minE/832644‑832780
|
| Alignment Legend |
|---|
Aligned base mismatch/match (shaded by quality score): ATCG/ATCG < 3 ≤ ATCG/ATCG < 14 ≤ ATCG/ATCG < 32 ≤ ATCG/ATCG < 36 ≤ ATCG/ATCG |
Unaligned base: atcg Masked matching base: atcg Alignment gap: ‑ Deleted base: ‑ |
GATK/CNVnator alignment
N/A
