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 F17 I0 R2
|
162 |
60.6 |
4616657 |
98.5% |
4547407 |
62.1 |
Breseq alignment
BRESEQ :: Evidence
|
| evidence |
seq id |
position |
mutation |
freq |
annotation |
gene |
description |
| RA |
W3110S.gb |
3,824,326 |
T→C |
100% |
pseudogene (459/687 nt) |
rph → |
ECK3633:JW3618:b3643; ribonuclease PH |
|
| |
seq id |
position |
ref |
new |
freq |
score (cons/poly) |
reads |
annotation |
genes |
product |
| * | W3110S.gb | 3,824,326 | 0 | T | C | 100.0%
| 228.0
/ NA
| 65 | pseudogene (459/687 nt) | rph | ECK3633:JW3618:b3643; ribonuclease PH |
| Reads supporting (aligned to +/- strand): ref base T (0/0); new base C (33/32); total (33/32) |
| Rejected as polymorphism: Frequency below/above cutoff threshold. |
| Rejected as polymorphism: Variant not supported by required number of reads on each strand. |
TGCCTGCGTGGCGCTGGTAGATGCGCTACAGAAGCTGGTGGAAAACGGCAAGCTGAAAACCAATCCGATGAAAGGGATGGTAGCCGCAGTTTCTGTCGGAATTGTGAACGGCGAAGCGGTTTGCGATCTGG > W3110S.gb/3824263‑3824393
|
tGCCTGCGTGGCGCTGGCAGATGCGCTACAGAAGCTGGTGGAAAACGGCAAGCTGAAAACCAACCCGATg > 1:1239292/1‑70 (MQ=255)
tGCCTGCGTGGCGCTGGCAGATGCGCTACAGAAGCTGGTGGAAAACGGCAAGCTGAAAACCAACCCGATGa < 1:339625/71‑1 (MQ=255)
tGCCTGCGTGGCGCTGGCAGATGCGCTACAGAAGCTGGTGGAAAACGGCAAGCTGAAAACCAACCCGATGa < 1:3879111/71‑1 (MQ=255)
gCCTGCGTGGCGCTGGCAGATGCGCTACAGAAGCTGGTGGAAAACGGCAAGCTGAAAACCAACCCGATGa > 1:1271076/1‑70 (MQ=255)
cTGCGTGGCGCTGGCAGATGCGCTACAGAAGCTGGTGGAAAACGGCAAGCTGAAAACCAACCCGATGAAAg > 1:2250745/1‑71 (MQ=255)
gCGTGGCGCTGGCAGATGCGCTACAGAAGCTGGTGGAAAACGGCAAGCTGAAAACCAACCCGAt < 1:4022811/64‑1 (MQ=255)
gCGTGGCGCTGGCAGATGCGCTACAGAAGCTGGTGGAAAACGGCAAGCTGAAAACCAACCCGATGAAAgg > 1:1154031/1‑70 (MQ=255)
gCGTGGCGCTGGCAGATGCGCTACAGAAGCTGGTGGAAAACGGCAAGCTGAAAACCAACCCGATGAAAgg > 1:2309631/1‑70 (MQ=255)
gTGGCGCTGGCAGATGCGCTACAGAAGCTGGTGGAAAACGGCAAGCTGAAAACCAACCCGATGAAAggg < 1:284914/69‑1 (MQ=255)
tGGCGCTGGCAGATGCGCTACAGAAGCTGGTGGAAAACGGCAAGCTGAAAACCAACCCGATGAAAggg < 1:2414368/68‑1 (MQ=255)
ggCGCTGGCAGATGCGCTACAGAAGCTGGTGGAAAACGGCAAGCTGAAAACCAACCCGATGAAAGGGATgg > 1:1639777/1‑71 (MQ=255)
gcgcTGGCAGATGCGCTACAGAAGCTGGTGGAAAACGGCAAGCTGAAAACCAACCCGATGAAAGGGATgg < 1:2338237/70‑1 (MQ=255)
gcgcTGGCAGATGCGCTACAGAAGCTGGTGGAAAACGGCAAGCTGAAAACCAACCCGATGAAAGGGATGGt < 1:3373147/71‑1 (MQ=255)
gcgcTGGCAGATGCGCTACAGAAGCTGGTGGAAAACGGCAAGCTGAAAACCAACCCGATGAAAGGGATGGt < 1:2154918/71‑1 (MQ=255)
cgcTGGCAGATGCGCTACAGAAGCTGGTGGAAAACGGCAAGCTGAAAACCAACCCGATGAAAGGGATGGTa < 1:4453680/71‑1 (MQ=255)
cgcTGGCAGATGCGCTACAGAAGCTGGTGGAAAACGGCAAGCTGAAAACCAACCCGATGAAAGGGATGGTa < 1:2468788/71‑1 (MQ=255)
gcTGGCAGATGCGCTACAGAAGCTGGTGGAAAACGGCAAGCTGAAAACCAACCCGATGAAAGGGATGGTAg > 1:302915/1‑71 (MQ=255)
cTGGCAGATGCGCTACAGAAGCTGGTGGAAAACGGCAAGCTGAAAACCAACCCGATGAAAGGGATgg < 1:537993/67‑1 (MQ=255)
ggcaGATGCGCTACAGAAGCTGGTGGAAAACGGCAAGCTGAAAACCAACCCGATGAAAGGGATGGTAGCCg > 1:4276610/4‑71 (MQ=255)
gcaGATGCGCTACAGAAGCTGGTGGAAAACGGCAAGCTGAAAACCAACCCGATGaa < 1:4069487/54‑1 (MQ=255)
gcaGATGCGCTACAGAAGCTGGTGGAAAACGGCAAGCTGAAAACCAACCCGATGAAAGGGATGGTAGCCGc < 1:1744779/69‑1 (MQ=255)
gATGCGCTACAGAAGCTGGTGGAAAACGGCAAGCTGAAAACCAACCCGATGAAAGGGATGGTAGCCGCAGt < 1:710687/71‑1 (MQ=255)
aTGCGCTACAGAAGCTGGTGGAAAACGGTAAGCTGAAAACCAACCCGATGAAAGGGATGGTAGCCGCAGt > 1:650594/1‑70 (MQ=255)
aTGCGCTACAGAAGCTGGTGGAAAACGGCAAGCTGAAAACCAACCCGATGAAAGGGATGGTa > 1:4075394/1‑62 (MQ=255)
aTGCGCTACAGAAGCTGGTGGAAAACGGCAAGCTGAAAACCAACCCGATGAAAGGGATGGTAGCCGCAg > 1:1277233/1‑69 (MQ=255)
tGCGCTACAGAAGCTGGTGGAAAACGGCAAGCTGAAAACCAACCCGATGaaa > 1:2005522/1‑52 (MQ=255)
tGCGCTACAGAAGCTGGTGGAAAACGGCAAGCTGAAAACCAACCCGATGAAAGGGATGGTAGCCGCAGttt > 1:2160144/1‑71 (MQ=255)
cgcTACAGAAGCTGGTGGAAAACGGCAAGCTGAAAACCAACCCGATGAAAGGGATGGTa < 1:3553571/59‑1 (MQ=255)
gcTACAGAAGCTGGTGGAAAACGGCAAGCTGAAAACCAACCCGATGAAAg < 1:2554070/50‑1 (MQ=255)
gcTACAGAAGCTGGTGGAAAACGGCAAGCTGAAAACCAACCCGATGAAAGGGATGGTAGCCGCAGTTTCTg > 1:1185864/1‑71 (MQ=255)
cTACAGAAGCTGGTGGAAAACGGCAAGCTGAAAACCAACCCGATGAAAGGGATGGTAGCCGCAGTTTCTGt < 1:4013895/71‑1 (MQ=255)
tACAGAAGCTGGTGGAAAACGGCAAGCTGAAAACCAACCCGATGAAAggg > 1:3063250/1‑50 (MQ=255)
cAGAAGCTGGTGGAAAACGGCAAGCTGAAAACCAACCCGATGAAAGGGa < 1:3020336/49‑1 (MQ=255)
cAGAAGCTGGTGGAAAACGGCAAGCTGAAAACCAACCCGATGAAAGGGATg > 1:778260/1‑51 (MQ=255)
cAGAAGCTGGTGGAAAACGGCAAGCTGAAAACCAACCCGATGAAAGGGATGGTAg < 1:1900566/55‑1 (MQ=255)
cAGAAGCTGGTGGAAAACGGCAAGCTGAAAACCAACCCGATGAAAGGGATGGTAGCCGCAGTTTCTGTc < 1:1326391/69‑1 (MQ=255)
cAGAAGCTGGTGGAAAACGGCAAGCTGAAAACCAACCCGATGAAAGGGATGGTAGCCGCAGTTTCTGTCgg > 1:1778272/1‑71 (MQ=255)
cAGAAGCTGGTGGAAAACGGCAAGCTGAAAACCAACCCGATGAAACGGATGGTAGCCGCAGttt > 1:1812328/1‑64 (MQ=255)
gAAGCTGGTGGAAAACGGCAAGCTGAAAACCAACCCGATGAAAGGGATGGTAGCCGCAGTTTCTGTCggta < 1:176531/71‑3 (MQ=255)
gAAGCTGGTGGAAAACGGCAAGCTGAAAACCAACCCGATGAAAGGGATGGTAGCCGCAGTTTCTGTCggta > 1:3435116/1‑69 (MQ=255)
aGCTGGTGGAAAACGGCAAGCTGAAAACCAACCCGATGAAAGGGATGGTAGCCGCAGTTTCTGTCGGTAtt > 1:3427834/1‑71 (MQ=255)
gCTGGTGGAAAACGGCAAGCTGAAAACCAACCCGATGAAAGGGATGGTAGCCGCAGTTTCt > 1:3016499/1‑61 (MQ=255)
tggtggAAAACGGCAAGCTGAAAACCAACCCGATGaa < 1:1722733/37‑1 (MQ=255)
tggtggAAAACGGCAAGCTGAAAACCAACCCGATGAAAGGGATGGTAGCCGCAGTTTCt > 1:2429503/1‑59 (MQ=255)
ggtggAAAACGGCAAGCTGAAAACCAACCCGATGAAAGGGATGGTAGCCGCAGTTTCTGTCGGTATtgta > 1:2577600/1‑69 (MQ=255)
ggtggAAAACGGCAAGCTGAAAACCAACCCGATGAAAGGGATGGTAGCCGCAGTTTCTGTCGGTATtgta > 1:4498110/1‑69 (MQ=255)
gtggAAAACGGCAAGCTGAAAACCAACCCGATGAAAGGGATGGTAGCCGCAGTTTCTGTCGGTATTGTaaa > 1:4207383/1‑71 (MQ=255)
aaaaCGGCAAGCTGAAAACCAACCCGATGAAAGGGATGGTAGCCGCAGTTTCTGTCGGTATTGTAAACggt < 1:4312769/71‑2 (MQ=255)
aCGGCAAGCTGAAAACCAACCCGATGAAAGGGATGGTAGCCGCAGTTTCTGTCGGTATTGTAAACggtg > 1:438505/1‑67 (MQ=255)
gCAAGCTGAAAACCAACCCGATGAAAGGTATGGTAGCCGCAGTTTCTGTCGGTATTGTAAACGGTGAAGca < 1:834686/71‑2 (MQ=255)
gCAAGCTGAAAACCAACCCGATGAAAGGGATGGTAGCCACAGTTTCTGTCGGTATTGTAAACGGTGAAGca < 1:1203430/71‑2 (MQ=255)
cAAGCTGAAAACCAACCCGATGAAAGGGATGGTAg < 1:3094903/35‑1 (MQ=255)
aaGCTGAAAACCAACCCGATGAAAGGGATGGTAGc < 1:542195/35‑1 (MQ=255)
aaGCTGAAAACCAACCCGATGAAAGGGATGGTAGCCGCAGTTTCTGt > 1:2076478/1‑47 (MQ=255)
aaGCTGAAAACCAACCCGATGAAAGGGATGGTAGCCGCAGTTTCTGTCGGTATTGTAAACGGTGAAGcaat < 1:140021/71‑4 (MQ=255)
cTGAAAACCAACCCGATGAAAGGGATGGTAGCCGCAGTTTCTGTCGGTATTGTAAACGGTGAAGcaat < 1:1717685/68‑4 (MQ=255)
cTGAAAACCAACCCGATGAAAGGGATGGTAGCCGCAGTTTCTGTCGGTATTGTAAACGGTGAAGCAATTTg > 1:4091924/1‑71 (MQ=255)
gAAAACCAACCCGATGAAAGGGATGGTAGCCGCAg > 1:529214/1‑35 (MQ=255)
aaaaCCAACCCGATGAAAGGGATGGTAGCCGCAGTTTCTGTCGGTAtt > 1:96296/1‑48 (MQ=39)
aaaaCCAACCCGATGAAAGGGATGGTAGCCGCAGTTTCTGTCGGTATTGTaaa > 1:2805649/1‑53 (MQ=255)
aaaCCAACCCGATGAAAGGGATGGTAGCCGCAGTTTCTGTCgg > 1:4593621/1‑43 (MQ=255)
aaaCCAACCCGATGAAAGGGATGGTAGCCGCAGTTTCTGTCGGTATTGTAAACGGTGAAGCAATTTGCGAt > 1:2765275/1‑71 (MQ=255)
aCCAACCCGATGAAAGGGATGGTAGCCGCAGTTTCTGTCGGTATTGTAAACggt < 1:3230139/54‑2 (MQ=255)
ccAACCCGATGAAAGGGATGGTAGCCGCAGTTTCTGTCgg < 1:1411993/40‑1 (MQ=255)
cAACCCGATGAAAGGGATGGTAGCCGCAGTTTCTGTCGGTATTGTAAACGGTGAAGCAATTTGCGATCTgg < 1:2354774/71‑1 (MQ=255)
|
TGCCTGCGTGGCGCTGGTAGATGCGCTACAGAAGCTGGTGGAAAACGGCAAGCTGAAAACCAATCCGATGAAAGGGATGGTAGCCGCAGTTTCTGTCGGAATTGTGAACGGCGAAGCGGTTTGCGATCTGG > W3110S.gb/3824263‑3824393
|
| 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
