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 |
|
A12 F1 I2 R1
|
766 |
55.6 |
2631458 |
94.7% |
2491990 |
109.9 |
Breseq alignment
BRESEQ :: Evidence
|
| evidence |
seq id |
position |
mutation |
annotation |
gene |
description |
| RA |
NC_000913 |
1,594,132 |
(C)8→10 |
pseudogene (3856/3861 nt) |
yneO ← |
pseudogene, AidA homolog |
|
| |
seq id |
position |
ref |
new |
freq |
score (cons/poly) |
reads |
annotation |
genes |
product |
| * | NC_000913 | 1,594,124 | 1 | . | C | 97.3%
| 120.2
/ ‑3.8
| 37 | pseudogene (2/1461 nt) | yneO | pseudogene, AidA homolog |
| Reads supporting (aligned to +/- strand): ref base . (1/0); new base C (15/21); total (16/21) |
| Fisher's exact test for biased strand distribution p-value = 4.32e-01 |
| Kolmogorov-Smirnov test that lower quality scores support variant p-value = 9.94e-01 |
| * | NC_000913 | 1,594,124 | 2 | . | C | 97.3%
| 118.6
/ ‑3.8
| 37 | pseudogene (2/1461 nt) | yneO | pseudogene, AidA homolog |
| Reads supporting (aligned to +/- strand): ref base . (1/0); new base C (15/21); total (16/21) |
| Fisher's exact test for biased strand distribution p-value = 4.32e-01 |
| Kolmogorov-Smirnov test that lower quality scores support variant p-value = 9.94e-01 |
AACGTCATCAGGCCATTGTTTCCGGTATAGTTGCCGTTAACGGTCAGTACATTCCCCGGTTTCCCCCCTTCGCTATTCATTTGAACCGTGCCGCCATTCTCCAGGTTGCCGCCGATAGTGGTTTTAGCGACACGCAGT‑‑G‑‑CCCCCCC‑‑CAGGCATAACGTTCATATCACCTGCAGTGGTGACATTTCCCGACATCACACCGCTGTTATGGATATTAATGTGTTGACTTGCCATATTAATGGCAGAGTCGGAACC > NC_000913/1593986‑1594237
||
aaCGTCATCAGGCCATTGTTTCCGGTATAGTTGCCGTTAACGGTCAGTACATTCCCCGGTTTCCCCCCTTCGCTATTCATTTGAACCGTGCCGCCATTCTCCAGGTTGCCGCCGATAGTGGTTTTAGCGACACGCAGT‑‑g > 2:1201688/1‑139 (MQ=255)
gTCATCAGGCCATTGTTTCCGGTATAGTTGCCGTTAACGGTCAGTACATTCCCCGGTTTCCCCCCTTCGCTATTCATTTGAACCGTGCCGCCATTCTCCAGGTTGCCGCCGATAGTGGTTTTAGCGACACGCAGT‑‑G‑‑ccc < 1:1201688/139‑1 (MQ=255)
tcatcaGGCCATTGTTTCCGGTATAGTTGCCGTTAACGGTCAGTACATTCCCCGGTTTCCCCCCTTCGCTATTCATTTGAACCGTGCCGCCATTCTCCAGGTTGCCGCCGATAGTGGTTTTAGCGACACGCAGT‑‑G‑‑cccc < 2:1189630/139‑1 (MQ=255)
atcaGGCCATTGTTTCCGGTATAGTTGCCGTTAACGGTCAGTACATTCCCCGGTTTCCCCCCTTCGCTATTCATTTGAACCGTGCCGCCATTCTCCAGGTTGCCGCCGATAGTGGTTTTAGCGACACGCAGT‑‑G‑‑cccccc > 1:861739/1‑139 (MQ=255)
ttGTTTCCGGTATAGTTGCCGTTAACGGTCAGTACATTCCCCGGTTTCCCCCCTTCGCTATTCATTTGAACCGTGCCGCCATTCTCCAGGTTGCCGCCGATAGTGGTTTTAGCGACACGCAGT‑‑G‑‑ccccccc‑‑cccaggca < 1:716639/139‑8 (MQ=255)
tGTTTCCGGTATAGTTGCCGTTAACGGTCAGTACATTCCCCGGTTTCCCCCCTTCGCTATTCATTTGAACCGTGCCGCCATTCTCCAGGTTGCCGCCGATAGTGGTTTTAGCGACACGCAGT‑‑G‑‑ccccccc‑‑cccaggcat < 2:861739/139‑9 (MQ=255)
gTTTCCGGTATAGTTGCCGTTAACGGTCAGTACATTCCCCGGTTTCCCCCCTTCGCTATTCATTTGAACCGTGCCGCCATTCTCCAGGTTGCCGCCGATAGTGGTTTTAGCGACACGCAGT‑‑G‑‑ccccccc‑‑cccccaggca < 1:892591/139‑10 (MQ=255)
ataGTTGCCGTTAACGGTCAGTACATTCCCCGGTTTCCCCCCTTCGCTATTCATTTGAACCGTGCCGCCATTCTCCAGGTTGCCGCCGATAGTGGTTTTAGCGACACGCAGT‑‑GCCCCCCCCC‑‑CAGGCATAACGTTCata > 1:1113413/1‑139 (MQ=255)
ttGCCGTTAACGGTCAGTACATTCCCCGGTTTCCCCCCTTCGCTATTCATTTGAACCGTGCCGCCATTCTCCAGGTTGCCGCCGATAGTGGTTTTAGCGACACGCAGT‑‑GCCCCCCCCC‑‑CAGGCCTACCGTCCATATccc > 1:361078/1‑137 (MQ=255)
ttGCCGTTAACGGTCAGTACATTCCCCGGTTTCCCCCCTTCGCTATTCATTTGAACCGTGCCGCCATTCTCCAGGTTGCCGCCGATAGTGGTTTTAGCGACACGCAGT‑‑G‑‑ccccccc‑‑cc < 2:998575/118‑2 (MQ=255)
ttGCCGTTAACGGTCAGTACATTCCCCGGTTTCCCCCCTTCGCTATTCATTTGAACCGTGCCGCCATTCTCCAGGTTGCCGCCGATAGTGGTTTTAGCGACACGCAGT‑‑G‑‑ccccccc‑‑cc > 1:998575/1‑117 (MQ=255)
cGTTAACGGTCAGTACATTCCCCGGTTTCCCCCCTTCGCTATTCATTTGAACCGTGCCGCCATTCTCCAGGTTGCCGCCGATAGTGGTTTTAGCGACACGCAGT‑‑GCCCCCCCCC‑‑CAGGCATAACGTTCATATCACCTGc < 1:1273910/139‑1 (MQ=255)
cGTTAACGGTCAGTACATTCCCCGGTTTCCCCCCTTCGCTATTCATTTGAACCGTGCCGCCATTCTCCAGGTTGCCGCCGATAGTGGTTTTAGCGACACGCAGT‑‑GCCCCCCCCC‑‑CAGGCATAACGTTCATATCACCTGc < 1:752162/139‑1 (MQ=255)
aaCGGTCAGTACATTCCCCGGTTTCCCCCCTTCGCTATTCATTTGAACCGTGCCGCCATTCCCCAGGTTGCCGCCGATAGTGGTTTTAGCGACACGCAGT‑‑G‑‑CCCCCCCATCAGGCAGAACGTTCATATCACCTGccgcg > 2:1228321/1‑135 (MQ=255)
aCGGTCAGTACATTCCCCGGTTTCCCCCCTTCGCTATTCATTTGAACCGTGCCGCCATTCTCCAGGTTGCCGCCGATAGTGGTTTTAGCGACACGCAGT‑‑GCCCCCCCCC‑‑CAGGCATAACGTTCATATCACCGGCActgc > 2:1077398/1‑138 (MQ=255)
cGGTCAGTACATTCCCCGGTTTCCCCCCTTCGCTATTCATTCGAACCGTGCCGCCATTCTCCAGGTTGCCGCCGATAGTGGTTTTAGCGACACGCAGT‑‑GCCCCCCCCC‑‑CAGGCATAACGTTCATATCACCTGCAgtggt > 1:485257/1‑139 (MQ=255)
ttCCCCGGTTTCCCCCCTTCGCTATTCATTTGAACCGTGCCTCCATTCTCCAGGTTGCCGCCGATAGTGGTTTTAGCGACACGCAGT‑‑G‑‑ccccccc‑‑cc < 1:106822/97‑2 (MQ=255)
ttCCCCGGTTTCCCCCCTTCGCTATTCATTTGAACCGTGCCGCCATTCTCCCGGTTGCCGCCGATAGTGGTTTTAGCGACACGCAGT‑‑G‑‑ccccccc‑‑cc > 2:106822/1‑96 (MQ=255)
tCCCCGGTTTCCCCCCTTCGCTATTCATTTGAACCGTGCCGCCATTCTCCAGGTTGCCGCCGATAGTGGTTTTAGCGACACGCAGT‑‑GCCCCCCCCC‑‑CAGGCATAACGTTCATATCACCTGCAGTGGTGACATTTCCCGa > 1:887189/1‑139 (MQ=255)
tCCCCGGTTTCCCCCCTTCGCTATTCATTTGAACCGTGCCGCCATTCTCCAGGTTGCCGCCGATAGTGGTTTTAGCGACACGCAGT‑‑GCCCCCCCCC‑‑CAGGCATAACGTTCATATAACCTGCCGTGGTGAAATTTCCGGa > 1:961705/1‑139 (MQ=255)
tCCCCGGTTTCCCCCCTTCGCTATTCATTTGAACCGTGCCGCCATTCTCCAGGTTGCCGCCGATAGTGGTTTTAGCGACACGCAGT‑‑GCCCCCCCCC‑‑CAGGCATAACATTCATATCACCTGCAGTGGTGACATTTCCCGa > 1:872556/1‑139 (MQ=255)
ccGGTTTCCCCCCTTCGCTATTCATTCGAACCGTGCCGCCATTCTCCAGGTTGCCGCCGATAGTGGTTTTAGCGACACGCAGT‑‑GCCCCCCCCC‑‑CAGGCATAACGTTCATATCACCTGCAGTGGTGACATTTCCCGACAt < 2:485257/139‑1 (MQ=255)
ggTTTCCCCCCTTCGCTATTCATTTGAACCGTGCCGCCATTCTCCAGGTTGCCGCCGATAGTGGTTTTAGCGACACGCAGT‑‑G‑‑ccccccc‑‑cccaggcata > 1:1090721/1‑90 (MQ=255)
ggTTTCCCCCCTTCGCTATTCATTTGAACCGTGCCGCCATTCTCCAGGTTGCCGCCGATAGTGGTTTTAGCGACACGCAGT‑‑G‑‑ccccccc‑‑cccaggcata < 2:1090721/99‑10 (MQ=255)
ggTTTCCCCCCTACGCTATTCATTTGAACCGTGCCGCCATTCTCCAGGTTGCCGCCGATAGTGGTTTTAGCGACACGCAGT‑‑GCCCCCCCCC‑‑CAGGCATAACGTTCAGATCATCTGCAGTGGTGACATTTCCCGACATca < 2:782281/139‑1 (MQ=255)
ttCCCCCCTTTCCTTTTCATTTGAACCGTTCCGCCCTTCTCCAGGTTGCCGCCCATAATGGTTTTTGCGACACGCAGT‑‑GCCCCCCCCC‑‑CAGGCATAACGTTCATATCACCTGCAGTGGTGACATTTCCCGACATCacac < 2:961705/139‑1 (MQ=255)
ttCCCCCCTTCGCTATTCATTTGAACCGTGCCGCCATTCTCCAGGTTGCCGCCGATAGTGGTTTTAGCGACACGCAGT‑‑GCCCCCCCCC‑‑CAGGCATAACGTTCATATCACCTGCAGTGGTGACATTTCCCGACATCacac < 2:974635/139‑1 (MQ=255)
tCCCCCCTTCGCTATTCATTTGAACCGTGCCGCCATTCTCCAGGTTGCCGCCGATAGTGGTTTTAGCGACACGCAGT‑‑GCCCCCCCCC‑‑CAGGCATAACGTTCATATCACCTGCAGTGGTGACAt < 1:380493/123‑1 (MQ=255)
tCCCCCCTTCGCTATTCATTTGAACCGTGCCGCCATTCTCCAGGTTGCCGCCGATAGTGGTTTTAGCGACACGCAGT‑‑GCCCCCCCCC‑‑CAGGCATAACGTTCATATCACCTGCAGTGGTGACAt > 2:380493/1‑123 (MQ=255)
tcccccTTCGCTATTCATTTGAACCGTGCCGCCATTCTCCAGGTTGCCGCCGATAGTGGTTTTAGCGACACGCAGT‑‑GCCCCCCCCC‑‑CAGGCATAACGTTCATATCACCTGCAGTGGTGACATTTCCCGACATCACACCg < 2:1198926/138‑1 (MQ=255)
ccccccTTCGCTATTCTTTGGACCCGGCCCGCGATACTCAAGTTTGCGTCCGATAATGCTTTTAGGGCCACGCGGG‑‑GCCCCCCCCC‑‑CAGGCAGAACGTTCATATCACCTGCAGTGGTGACAATTCCCGACATCACACCg < 2:1057508/139‑1 (MQ=255)
ccccccTTCGCTATTCATTTGAACCGTGCCGCCATTCTCCAGGTTGCCGCCGATAGTTGTTTTAGCGACACGCAGT‑‑GCCCCCCCCC‑‑CAGGCATAACGTTCATATCACCTGCAGTGGTGACATTTCCCGACATCACACCg < 2:887189/139‑1 (MQ=255)
ccccccTTCGCTATTCATTTGAACCGTGCCGCCATTCTCCAGGTTGCCGCCGATAGTGGTTTTAGCGACACGCAGT‑‑GCCCCCCCCC‑‑CAGGCATAACGTTCATATCACCTGCAGTGGTGACATTTCCCGACATCACACCg < 1:721221/139‑1 (MQ=255)
ccccccTTCGCTATTCATTTGAACCGTGCCGCCATTCTCCAGGTTGCCGCCGATAGTGGTTTTAGCGACACGCAGT‑‑GCCCCCCCCC‑‑CAGGCATAACGTTCATATCACCTGCAGTGGTGACATTTCCCGACATCACACCg < 1:131410/139‑1 (MQ=255)
ccccccTTCGCTATTCATTTGAACCGTGCCGCCATTCTCCAGGTTGCCGCCGATAGTGGTTTTAGCGACACGCAGT‑‑GCCCCCCCCC‑‑CAGGCATAACGTTCATATCACCTGCAGTGGTGACATTTCCCGACATCACACCg < 1:1228321/139‑1 (MQ=255)
ccccTTCGCTATTCCTTTGAACCGTGCCCCCATTCTCCAGGTTGCCGCCGATAGTGGTTTTAGCGACACGCAGT‑‑GCCCCCCCCC‑‑CAGGCATAACGTTCATATCACCTGCAg < 2:767193/111‑1 (MQ=255)
ccccTTCGCTATTCATTTGAACCGTGCCGCCATTCTCCAGGTTGCCGCCGATAGTGGTTTTAGCGACACGCAGT‑‑GCCCCCCCCC‑‑CAGGCATAACGTTCATATCACCTGCAg > 1:767193/1‑111 (MQ=255)
cTTCGCTATTCATTTGAACCGTGCCGCCATTCTCCAGGTTGCCGCCGATAGTGGTTTTAGCGACACGCAGT‑‑GCCCCCCCCC‑‑CAGGCATAACGTTCATATCACCTGCAGTGGTGACATTTCCCGACATCACACCGCTGtt < 2:1113413/139‑1 (MQ=255)
cGCTATTCATTTGAACCGTGCCGCCATGCTCCAGGTTGCCGCCGATAGTGGTTTTAGCGACACGCAGT‑‑GCCCCCCCCC‑‑CACGGCTGAGCTTTATCTCACATGCATCGCTCACACTGCCCGACATCAAACCGCTGtgctg > 2:492419/1‑135 (MQ=255)
ttGAACCGTGCCGCCATTCTCCAGGTTGCCGCCGATAGTGGTTTTAGCGACACGCAGT‑‑GCCCCCCCCC‑‑CAGGCATAACGTTc < 2:197589/82‑1 (MQ=255)
ttGAACCGTGCCGCCATTCTCCAGGTTGCCGCCGATAGTGGTTTTAGCGACACGCAGT‑‑GCCCCCCCCC‑‑CAGGCATAACGTTc > 1:197589/1‑82 (MQ=255)
ccGTGCCGCCATTCTCCAGGTTGCCGCCGATAGTGGTTTTAGCGACACGCAGT‑‑G‑‑ccccccc‑‑cc < 2:333833/63‑2 (MQ=255)
ccGTGCCGCCATTCTCCAGGTTGCCGCCGATAGTGGTTTTAGCGACACGCAGT‑‑G‑‑ccccccc‑‑cc > 1:333833/1‑62 (MQ=255)
gTGCCGCCATTCTCAGCGTTGGAGCCGTTTGTGGTTTTAGCGACACGCAGTACC‑‑CCCCCCC‑‑CAGGCATAACGTTCATATCACCTGCAGTGATGACATTTCCCGACATCACACCGCTGTTATGGATATTAATGTGTTGAc < 2:1119720/139‑1 (MQ=255)
tGCCGCCATTCTCCAGGTTGCCGCCGATAGTGGTTTTAGCGACACGCAGT‑‑GCCCCCCCCC‑‑CAGGCATAACGTTCATATCACCTGCAGTGGTGACATTTCCCGACATCACACCGCTGTTAt < 1:614358/120‑1 (MQ=255)
tGCCGCCATTCTCCAGGTTGCCGCCGATAGTGGTTTTAGCGACACGCAGT‑‑GCCCCCCCCC‑‑CAGGCATAACGTTCATATCACCTGCAGTGGTGACATTTCCCGACATCACACCGCTGTTAt > 2:614358/1‑120 (MQ=255)
gccATTCTCCAGGTTGCCGCCGATAGTGGTTTTAGCGACACGCAGT‑‑GCCCCCCCCC‑‑CATGCATAACGTTCATATCACCTGCAGTGGTGACATTTCCCGACATCACACCGCTGTTATGGATATTAATGTGTTGACTTGcc < 2:1139039/139‑1 (MQ=255)
gccATTCTCCAGGTTGCCGCCGATAGTGGTTTTAGCGACACGCAGT‑‑GCCCCCCCCC‑‑CAGGCATAACGTTCATATCACCTGCAGTGGTGACATTTCCCGACATCACACCGCTGTTATGGATATTAATGTGTTGACTTGcc < 2:464908/139‑1 (MQ=255)
gccATTCTCCAGGTTGCCGCCGATAGTGGTTTTAGCGACACGCAGT‑‑GCCCCCCCCC‑‑CAGGCATAACGTTCATATCACCTGCAGTGGTGACATTTCCCGACATCACACCGCTGTTATGGATATTAATGTGTTGACTTGcc < 2:872556/139‑1 (MQ=255)
agacagcttcAGTTTGCCGCCGATAGTGGTTTTAGCGAACCGCAGT‑‑GCCCCCCCCC‑‑CAGGCATAACGTTCATATCACCTGCAGTGGTGACATTTCCCGACATCACACCTCTGTTATGGATATTAATGTGTTGACTTGcc < 2:1189257/130‑1 (MQ=255)
cgccgATAGTGGTTTTAGCGACACGCAGT‑‑GCCCCCCCCC‑‑CCGGCATAACGTTCATATCACCTGCAGGGGTGACATTTCCCGACATCACACAGCTGTTATGGATATTAATGTGTTGACTTGCCATATAAATGGcctgtct > 1:1189257/1‑133 (MQ=255)
cgccgATAGTGGTTTTAGCGACACGCAGT‑‑GCCCCCCCCC‑‑CAGGCATAACGTTCATATCACCTGCAGTGGTGACATTTcc < 2:1314582/79‑1 (MQ=255)
cgccgATAGTGGTTTTAGCGACACGCAGT‑‑GCCCCCCCCC‑‑CAGGCATAACGTTCATATCACCTGCAGTGGTGACATTTcc > 1:1314582/1‑79 (MQ=255)
tAGTGGTTTTAGCGACACGCAGT‑‑GCCCCCCCCC‑‑CAGGCATAACGTTCATATCACCGGCGGTGGTGACATTTCCCGACATCACACCGCTGTTATGGATATTAATGTGTTGACTTGCCATATTAATGACAGAGCCGAAAcc > 2:389217/1‑139 (MQ=255)
||
AACGTCATCAGGCCATTGTTTCCGGTATAGTTGCCGTTAACGGTCAGTACATTCCCCGGTTTCCCCCCTTCGCTATTCATTTGAACCGTGCCGCCATTCTCCAGGTTGCCGCCGATAGTGGTTTTAGCGACACGCAGT‑‑G‑‑CCCCCCC‑‑CAGGCATAACGTTCATATCACCTGCAGTGGTGACATTTCCCGACATCACACCGCTGTTATGGATATTAATGTGTTGACTTGCCATATTAATGGCAGAGTCGGAACC > NC_000913/1593986‑1594237
|
| Alignment Legend |
|---|
Aligned base mismatch/match (shaded by quality score): ATCG/ATCG < 3 ≤ ATCG/ATCG < 14 ≤ ATCG/ATCG < 25 ≤ ATCG/ATCG < 35 ≤ ATCG/ATCG < 40 ≤ ATCG/ATCG |
Unaligned base: atcg Masked matching base: atcg Alignment gap: ‑ Deleted base: ‑ |
GATK/CNVnator alignment
N/A
