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 F2 I200 R1
|
216 |
30.8 |
1683622 |
97.2% |
1636480 |
87.0 |
Breseq alignment
BRESEQ :: Evidence
|
| evidence |
seq id |
position |
mutation |
annotation |
gene |
description |
| RA |
NZ_CP009273 |
510,152 |
Δ1 bp |
coding (164/459 nt) |
ybbJ ← |
NfeD family protein |
|
| |
seq id |
position |
ref |
new |
freq |
score (cons/poly) |
reads |
annotation |
genes |
product |
| * | NZ_CP009273 | 510,151 | 0 | C | . | 80.0%
| 31.8
/ 9.6
| 15 | coding (165/459 nt) | ybbJ | NfeD family protein |
| Reads supporting (aligned to +/- strand): ref base C (2/1); new base . (7/5); total (9/6) |
| Fisher's exact test for biased strand distribution p-value = 1.00e+00 |
| Kolmogorov-Smirnov test that lower quality scores support variant p-value = 1.00e+00 |
CGCCGCGACAACCATTTCCACCACAGCCAGGCGGCGAGCAGCGTCAGGATGGCAAACATTACCCCTTGCCACTCCCAACCCAGCGGCACCAGCCAGACCACCAGGCCGGTAATCACCGCTGCCACGCCGCTCCACAACAAATAACCATTTCCGCCC > NZ_CP009273/510083‑510238
|
cgccgcGACAACCATTTCCACCACAGCCAGGCGGCGAGCAGCGTCAGGATGGCAAACATTACCCCTTG‑CACTCCCAACCCAGCGGCAcca < 1:677251/90‑1 (MQ=255)
ccATTTCCACCACAGCCAGGCGGCGAGCAGCGTCAGGATGGCAAACATTCCCCCTTG‑CACTCCCAACCCAGCGGCACCAGCCAGaccacc < 2:198400/90‑1 (MQ=255)
ttCCACCACAGCCAGGCGGCGAGCAGCGTCAGGATGGCAAACATTACCCCTTG‑CACTCCCAACCCAGCGGCACCAGCCAGACCACCAGGc < 2:782002/90‑1 (MQ=255)
cacaGCCAGGCGGCGAGCAGCGTCAGGATGGCAAACATTACCCCTTGCCa > 1:708931/1‑50 (MQ=255)
cacaGCCAGGCGGCGAGCAGCGTCAGGATGGCAAACATTACCCCTTGCCa < 2:708931/50‑1 (MQ=255)
aGCCAGGCGGCGAGCAGCGTCAGGATGGCAAACATTACCCCTTG‑CACTCCCAACCCAGCGGCACCAGCCAGACCACCAGGCCGGTAATCa > 2:681948/1‑90 (MQ=255)
ccAGGCGGCGAGCAGCGTCAGGATGGCAAACATTACCCCTTG‑CACTCCCAACCCAGCGGCACCAGCCAGACCACCAGGCCGGTAATCAcc < 1:708663/90‑1 (MQ=255)
agcGTCAGGATGGCAAACATTACCCCTTG‑CACTCCCAACCCAGCGGCACCAGCCAGACCACCAGGCCGGTAATCACCGCTGCCAcgccgc > 2:822524/1‑90 (MQ=255)
ggCAAACATTACCCCTTG‑CACTCCCAACCCAGCGGCa > 1:491883/1‑37 (MQ=38)
ggCAAACATTACCCCTTG‑CACTCCCAACCCAGCGGCa < 2:491883/37‑1 (MQ=38)
cATTACCCCTTG‑CACTCCCAACCCAGCGGCACCAGCCAGACCACCAGGCCGGTAATCACCGCTGCCACGCCGCTCCACAACAAATAACCa > 1:245015/1‑90 (MQ=255)
cATTACCCCTTG‑CACTCCCAACCCAGCGGCACCAGCCAGACCACCAGGCCGGTAATCACCGCTGCCACGCCGCTCCACAACAAATAACCa > 2:28454/1‑90 (MQ=255)
aCCCCTTG‑CACTCCCAACCCAGCGGCACCAGCCAGACCACCAGGCCGGTAATCACCGCTGCCACGCCGCTCCACAACAAATAACCATTTc > 1:722964/1‑90 (MQ=255)
aCCCCTTG‑CACTCCCAACCCAGCGGCACCAGCCAGACCACCAGGCCGGTAATCACCGCTGCCACGCCGCTCCACAACAAATAACCATTTc > 1:785011/1‑90 (MQ=255)
tGCCACTCCCAACCCAGCGGCACCAGCCAGACCACCAGGCCGGTAATCACCGCTGCCACGCCGCTCCACAACAAATAACCATTTCCGccc > 1:725528/1‑90 (MQ=255)
|
CGCCGCGACAACCATTTCCACCACAGCCAGGCGGCGAGCAGCGTCAGGATGGCAAACATTACCCCTTGCCACTCCCAACCCAGCGGCACCAGCCAGACCACCAGGCCGGTAATCACCGCTGCCACGCCGCTCCACAACAAATAACCATTTCCGCCC > NZ_CP009273/510083‑510238
|
| Alignment Legend |
|---|
Aligned base mismatch/match (shaded by quality score): ATCG/ATCG < 3 ≤ ATCG/ATCG < 23 ≤ ATCG/ATCG < 29 ≤ ATCG/ATCG < 35 ≤ ATCG/ATCG < 41 ≤ ATCG/ATCG |
Unaligned base: atcg Masked matching base: atcg Alignment gap: ‑ Deleted base: ‑ |
GATK/CNVnator alignment
BRESEQ :: bam2aln output
CGCCGCGACAACCATTTCCACCACAGCCAGGCGGCGAGCAGCGTCAGGATGGCAAACATTACCCCTTGCCACTCCCAACCCAGCGGCACCAGCCAGACCACCAGGCCGGTAATCACCGCTGCCACGCCGCTCCACAACAAATAACCATTTCCGCCCAGCATCT > NZ_CP009273/510083‑510245
|
CGCCGCGACAACCATTTCCACCACAGCCAGGCGGCGAGCAGCGTCAGGATGGCAAACATTACCCCTTG‑CACTCCCAACCCAGCGGCACCAGCCAGACCAC < SRR3722079.684359/100‑1 (MQ=60)
CCATTTCCACCACAGCCAGGCGGCGAGCAGCGTCAGGATGGCAAACATTACCCCTTGCCACTCCCAACCCctgtctcttatacacatctccgagcccccg > SRR3722079.716459/1‑70 (MQ=60)
CCAGGCGGCGAGCAGCGTCAGGATGGCAAACATTACCCCTTG‑CACTCCCAACCCAGCGGCACCAGCCAGACCACCAGGCCGGTAATCACCGCTGCCACGC < SRR3722079.716186/100‑1 (MQ=60)
GCGTCAGGATGGCAAACATTACCCCTTG‑CACTCCCAACCCAGCGGCACCAGCCAGACCtgtctcttatacacatctccgagcccacgagaccagagagga > SRR3722079.496223/1‑58 (MQ=60)
GGATGGCAAACATTACCCCTTG‑CACTCCCAACCCAGCGGCACCAGCCAGACCACCAGGCCGGTAATCACCGCTGCCACGCCGCTCCACAACAAATAACCA > SRR3722079.247080/1‑100 (MQ=60)
GGCAAACATTACCCCTTG‑CACTCCCAACCCAGCGGCACCAGCCAGACCACCAGGCCGGTAATCACCGCTGCCACGCCGCTCCACAACAAATAACCATTTC > SRR3722079.730690/1‑100 (MQ=60)
GGCAAACATTACCCCTTG‑CACTCCCAACCCAGCGGCACCAGCCAGACCACCAGGCCGGTAATCACCGCTGCCACGCCGCTCCACAACAAATAACCATTTC > SRR3722079.793432/1‑100 (MQ=60)
ACATTACCCCTTG‑CACTCCCAACCCAGCGGCACCAGCCAGACCACCAGGCCGGTAATCACCGCTGCCACGCCGCTCCACAACAAATAACCATTTCCGCCC > SRR3722079.206562/1‑100 (MQ=60)
ACATTACCCCTTG‑CACTCCCAACCCAGCGGCACCAGCCAGACCACCAGGCCGGTAATCACCGCTGCCACGCCGCTCCACAACAAATAACCATTTCCGCCC > SRR3722079.293888/1‑100 (MQ=60)
gagacagcccttgCACTCCCAACCCAGCGGCACCAGCCAGACCACCAGGCCGGTAATCACCGCTGCCACGCCGCTCCACAACAAATAACCATTTCCGCCC < SRR3722079.336752/87‑1 (MQ=60)
CATTACCCCTTGCCACTCCCAACCCAGCGGCACCAGCCAGACCACCAGGCCGGTAATCACCGCTGCCACGCCGCTCCACAACAAATAACCATTTCCGCCC > SRR3722079.733290/1‑100 (MQ=60)
CCCCTTG‑CACTCCCAACCCAGCGGCACCAGCCAGACCACCAGGCCGGctgtctcttatacacatctccgagcccacgagaccagagaggatctcgtatgc > SRR3722079.92655/1‑47 (MQ=60)
CCCTTG‑CACTCCCAACCCAGCGGCACCAGCCAGACCACCAGGCCGGTAATCACCGCTGCCACGCCGCTCCACAACAAATAACCATTTCCGCCCAGCATCT > SRR3722079.13666/1‑100 (MQ=60)
|
CGCCGCGACAACCATTTCCACCACAGCCAGGCGGCGAGCAGCGTCAGGATGGCAAACATTACCCCTTGCCACTCCCAACCCAGCGGCACCAGCCAGACCACCAGGCCGGTAATCACCGCTGCCACGCCGCTCCACAACAAATAACCATTTCCGCCCAGCATCT > NZ_CP009273/510083‑510245
|
| Alignment Legend |
|---|
Aligned base mismatch/match (shaded by quality score): ATCG/ATCG < 0 ≤ ATCG/ATCG < 24 ≤ ATCG/ATCG < 30 ≤ ATCG/ATCG < 35 ≤ ATCG/ATCG < 41 ≤ ATCG/ATCG |
Unaligned base: atcg Masked matching base: atcg Alignment gap: ‑ Deleted base: ‑ |
