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 F21 I0 R2
|
316 |
65.6 |
5147759 |
97.4% |
5013917 |
60.3 |
Breseq alignment
BRESEQ :: Evidence
|
| evidence |
seq id |
position |
mutation |
freq |
annotation |
gene |
description |
| RA |
W3110S.gb |
3,824,533:1 |
+G |
100% |
pseudogene (666/687 nt) |
rph → |
ECK3633:JW3618:b3643; ribonuclease PH |
|
| |
seq id |
position |
ref |
new |
freq |
score (cons/poly) |
reads |
annotation |
genes |
product |
| * | W3110S.gb | 3,824,533 | 1 | . | G | 97.5%
| 135.0
/ ‑3.7
| 40 | pseudogene (666/687 nt) | rph | ECK3633:JW3618:b3643; ribonuclease PH |
| Reads supporting (aligned to +/- strand): ref base . (0/1); new base G (19/20); total (19/21) |
| Fisher's exact test for biased strand distribution p-value = 1.00e+00 |
| Kolmogorov-Smirnov test that lower quality scores support variant p-value = 9.95e-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. |
| Rejected as polymorphism: Polymorphic indel expands or contracts a homopolymer stretch. |
CAGGGGACGGCAGAAGGCGAGCCGTTCACCCATGAAGAGCTACTCATCTTGTTGGCTCTGGCCCGA‑G‑GGGAATCGAATCCATTGTAGCGACGCAGAAGGCGGCGCTGGCAAACTGATTTTTAAGGCGACT > W3110S.gb/3824468‑3824597
|
cAGGGGACGGCAGAAGGCGAGCCGTTCACCCATGAAGAGCTACTCACCTTGTTGGCGCTGGCCCGA‑g‑ggg > 1:3721371/1‑70 (MQ=255)
ggggACGGCAGAAGGCGAGCCGTTCACCCATGAAGAGCTACTCACCTTGTTGGCGCTGGCCCGA‑g‑ggggaa > 1:1168623/1‑68 (MQ=255)
ggACGGCAGAAGGCGAGCCGTTCACCCATGAAGAGCTACTCACCTTGTTGGCGCTGGCCCGA‑g‑ggg > 1:3405667/1‑66 (MQ=255)
aGAAGGCGAGCCGTTCACCCATGAAGAGCTACTCACCTTGTTGGCGCTGGCCCGA‑g‑gggg > 1:2085607/1‑59 (MQ=255)
gAAGGCGAGCCGTTCACCCATGAAGAGCTACTCACCTTGTTGGCGCTGGCCCGAGG‑GGGAATCGAATCCAt < 1:879039/71‑1 (MQ=255)
ggCGAGCCGTTCACCCATGAAGAGCTACTCACCTTGTTGGCGCTGGCCCGAGG‑GGGAATCGAATCCATTGt < 1:3656726/71‑1 (MQ=255)
gCCGTTCACCCATGAAGAGCTACTCACCTTGTTGGCGCGGGCCCGA‑GTGGGAATCGAATCCATTGTAGCg < 1:1530798/70‑1 (MQ=255)
ccGTTCACCCATGAAGAGCTACTCACCTTGTTGGCGCTGGCCCGAGG‑GGGAATCGAATCCATTGTAGCg < 1:857031/69‑1 (MQ=255)
ccGTTCACCCATGAAGAGCTACTCACCTTGTTGGCGCTGGCCCGAGG‑GGGAATCGAATCCATTGTAGCg < 1:567631/69‑1 (MQ=255)
ccGTTCACCCATGAAGAGCTACTCACCTTGTTGGCGCTGGCCCGAGG‑GGGAATCGAATCCATTGTAGCg < 1:1945019/69‑1 (MQ=255)
ccGTTCACCCATGAAGAGCTACTCACCTTGTTGGCGCTGGCCCGAGG‑GGGAATCGAATCCATTGTAGCGAc > 1:3987079/1‑71 (MQ=255)
ttCACCCATGAAGAGCTACTCACCTTGTTGGCGCTGGCCCGAGG‑GGGAATCGAATCCATTGTAGCGACGCa < 1:5073320/71‑1 (MQ=255)
cACCCATGAAGAGCTACTCACCTTGTTGGCGCTGGCCCGAGG‑GGgaatcga > 1:1425469/1‑51 (MQ=255)
cACCCATGAAGAGCTACTCACCTTGTTGGCGCTGGCCCGAGG‑GGGAATCGAATCCATTGTAGCGACGc > 1:1024424/1‑68 (MQ=255)
cACCCATGAAGAGCTACTCACCTTGTTGGCGCTGGCCCGAGG‑GGGAATCGAATCCATTGTAGCGACGCAg < 1:344011/70‑1 (MQ=255)
cACCAATGAAGAGCTACTCACCTTGTTGGCGCTGGCCCGAGG‑GGGAATCGAATCCATTGTAGCGACGc > 1:3730094/1‑68 (MQ=255)
aTGAAGAGCTACTCACCTTGTTGGCGCTGGCCCGAGG‑GGGAATCGAATCCATTGTAGCGACGCAGAAggcg > 1:2811059/1‑71 (MQ=255)
tGAAGAGCTACTCACCTTGTTGGCGCTGGCCCGA‑g‑gggga < 1:4557815/40‑3 (MQ=37)
aaGAGCTACTCACCTTGTTGGCGCTGGCCCGAGG‑GGGAATCTAATCCATTGTAGCGACGCAGAAGgcggcg < 1:4102588/71‑1 (MQ=255)
aaGAGCTACTCACCTTGTTGGCGCTGGCCCGAGG‑GGGAATCGAATCCATTGTAGCGACGCAGAAGgcggcg > 1:2437565/1‑71 (MQ=255)
gagCTACTCACCTTGTTGGCGCTGGCCCGAGG‑GGGAATCGAATCCATTGTAGCGACGCAGAAGGCGGCGCt < 1:1234289/71‑1 (MQ=255)
agCTACTCACCTTGTTGGCGCTGGCCCGAGG‑GGGAATCGAATCCATTGTAGCGACGCAGAAGGCGGCGCTg > 1:1049439/1‑71 (MQ=255)
cTACTCACCTTGTTGGCGCTGGCCCGAGG‑GGGAATCGAATCCATTGTAGCGACGCAGAAggcgg > 1:3666631/1‑64 (MQ=255)
tACTCACCTTGTTGGCGCTGGCCCGAGG‑GGGAATCGAATCCATTGTAGCGACGCAGAAggc < 1:3083935/61‑1 (MQ=255)
tACTCACCTTGTTGGCGCTGGCCCGAGG‑GGGAATCGAATCCATTGTAGCGACGCAGAAGGCGGCGCTGGc < 1:377164/70‑1 (MQ=255)
tCACCTTGTTGGCGCTGGCCCGAGG‑GGgaatcgaat > 1:2029082/1‑36 (MQ=19)
accTTGTTGGCGCTGGCCCGAGG‑GGGAATCGAATCCATTGTAGCGACGCAGaa > 1:2315271/3‑53 (MQ=255)
accTTGTTGGCGCTGGCCCGAGG‑GGGAATCGAATCCATTGTAGCGACGCAGaa > 1:549954/3‑53 (MQ=255)
accTTGTTGGCGCTGGCCCGAGG‑GGGAATCGAATCCATTGTAGCGACGCAGAAGGCGGCGCTGGCAAACt > 1:2844055/3‑70 (MQ=255)
accTTGTTGGCGCTGGCCCGAGG‑GGGAATCGAATCCATTGTAGCGACGCAGAAGGCGGCGCTGGCAAACt > 1:4213413/3‑70 (MQ=255)
ccTTGTTGGCGCTGGCCCGAGG‑GGGAATCGAATCCATTGTAGCGACGCAGAAGGCGGCGCTGGCAAACTGa < 1:711061/70‑1 (MQ=255)
ttgttgGCGCTGGCCCGAGG‑GGGAATCGAATCCATTGTAg > 1:4035992/1‑40 (MQ=37)
tgttgGCGCTGGCCCGAGG‑GGGAATCGAATCCATTGTAGCGACGCAGAAGGCGGCGCTGGc < 1:383083/61‑1 (MQ=255)
tgttgGCGCTGGCCCGAGG‑GGGAATCGAATCCATTGTAGCGACGCAGAAGGCGGCGCTGGCAAACTGAttt > 1:1547872/1‑71 (MQ=255)
ggCGCTGGCCCGAGG‑GGGAATCGAATCCATTGTAGAGACGCAGAAggcg > 1:2141393/1‑49 (MQ=255)
gcgctGGCCCGAGG‑GGGAATCGAATCCATTGTAGCGACGCAGAAGGCGGCGCTGGCAAACTGATTTTTaa < 1:2183869/67‑1 (MQ=255)
cgctGGCCCGAGG‑GGGAATCGAATCCATTGTAGCGACGCAGAAGGCGGCGCTGGCAAACTGAtt > 1:3956374/3‑64 (MQ=255)
gctGGCCCGAGG‑GGGAATCGAATCCATTGTAGCGACGCAGAAggc < 1:2092001/44‑1 (MQ=255)
gctGGCCCGAGG‑GGGAATCGAATCCATTGTAGCGACGCAGAAGGCGGCGCTGGCAAACt < 1:1779919/58‑1 (MQ=255)
gctGGCCCGAGG‑GGGAATCGAATCCATTGTAGCGACGCAGAAGGCGGCGCTGGCAAACTGAtt > 1:3376721/2‑63 (MQ=255)
ctGGCCCGAGG‑GGGAATCGAATCCATTGTAGCGACGCAGAAGGCGGCGCTGGCAAACTGATTTTTAAGGc > 1:3241580/1‑70 (MQ=255)
tGGCCCGAGG‑GGGAATCGAATCCATTGTAGCGACGCAGAAGGCGGCGCTGGCAAACTGATTTTTaa < 1:2630245/66‑1 (MQ=255)
gCCCGAGG‑GGGAATCGAATCCATTGTAGCGACGCAGAAGGCGGCGCTGGCAAACTGATTTTTAAGGCGACt < 1:1467001/71‑1 (MQ=255)
gCCCGAGG‑GGGAATCGAATCCATTGTAGCGACGCAGAAGGCGGCGCTGGCAAACTGATTTTTAAGGCGACt < 1:1182167/71‑1 (MQ=255)
cccGAGG‑GGGAATCGAATCCATTGTAGCGACGCAGAAGGCGGCGCTGGCAAACTGAt < 1:4464939/57‑1 (MQ=255)
|
CAGGGGACGGCAGAAGGCGAGCCGTTCACCCATGAAGAGCTACTCATCTTGTTGGCTCTGGCCCGA‑G‑GGGAATCGAATCCATTGTAGCGACGCAGAAGGCGGCGCTGGCAAACTGATTTTTAAGGCGACT > W3110S.gb/3824468‑3824597
|
| 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
