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 I227 R1
|
223 |
21.3 |
1167702 |
97.0% |
1132670 |
86.4 |
Breseq alignment
BRESEQ :: Evidence
|
| evidence |
seq id |
position |
mutation |
annotation |
gene |
description |
| RA |
NZ_CP009273 |
2,358,446 |
Δ1 bp |
coding (414/426 nt) |
nudI → |
nucleoside triphosphatase NudI |
|
| |
seq id |
position |
ref |
new |
freq |
score (cons/poly) |
reads |
annotation |
genes |
product |
| * | NZ_CP009273 | 2,358,444 | 0 | A | . | 90.9%
| 68.0
/ 4.8
| 22 | coding (412/426 nt) | nudI | nucleoside triphosphatase NudI |
| Reads supporting (aligned to +/- strand): ref base A (1/1); new base . (13/7); total (14/8) |
| Fisher's exact test for biased strand distribution p-value = 1.00e+00 |
| Kolmogorov-Smirnov test that lower quality scores support variant p-value = 1.68e-01 |
AAGAGTTTCAGGACTACGCGTGGGTAAAACCTGAAGATCTGGTGCATTATGATTTGAATGTCGCCACCCGAAAAACGTTACGTTTGAAAGGTCTTCTGTAACAATGATGACAGCCATTACTGGCTGTCAGATTGAAAATTTAGTGGTTAACGAATTCCC > NZ_CP009273/2358358‑2358516
|
aaGAGTTTCAGGACTACGCGTGGGTAAAACCTGAAGATCTGGTGCATTATGATTTGAATGTCGCCACCCGAAAAACGTTACGTTTGaagg < 1:170180/90‑3 (MQ=255)
tttCAGGACTACGCGTGGGTAAAACCTGAAGATCTGGTGCATTATGATTTGAATGTCGCCACCCGAAAAACGTTACGTTTG‑AAGGtcttc < 2:341494/90‑1 (MQ=255)
ttCAGGACTACGCGTGGGTAAAACCTGAAGATCTGGTGCATTATGATTTGAATGTCGCCACCCGAAAAACGTTACGTTTG‑AAGGtcttct < 2:133039/90‑1 (MQ=255)
tACGCGTGGGTAAAACCTGAAGATCTGGTGCATTATGATTTGAATGTCGCCACCCGAAAAACGTTACGTTTG‑AAGGTCTTCTGTAACAat > 2:105196/1‑90 (MQ=255)
aCGCGTGGGTAAAACCTGAAGATCTGGTGCATTATGATTTGAATGTCGCCACCCGAAAAACGTTACGTTTG‑AAGGTCTTCTGTAACAatg > 1:272286/1‑90 (MQ=255)
aCGCGTGGGTAAAACCTGAAGATCTGGTGCATTATGATTTGAATGTCGCCACCCGAAAAACGTTACGTTTG‑AAGGTCTTCTGTAACAatg > 1:386225/1‑90 (MQ=255)
aCGCGTGGGTAAAACCTGAAGATCTGGTGCATTATGATTTGAATGTCGCCACCCGAAAAACGTTACGTTTG‑AAGGTCTTCTGTAACAatg > 1:500336/1‑90 (MQ=255)
aCGCGTGGGTAAAACCTGAAGATCTGGTGCATTATGATTTGAATGTCGCCACCCGAAAAACGTTACGTTTG‑AAGGTCTTCTGTAACAatg > 2:360452/1‑90 (MQ=255)
gTGGGTAAAACCTGAAGATCTGGTGCATTATGATTTGAATGTCGCCACCCGAAAAACGTTACGTTTG‑AAGGTCTTCTGTAACAAtgatga < 1:451755/90‑1 (MQ=255)
tGGGTAAAACCTGAAGATCTGGTGCATTATGATTTGAATGTCGCCACCCGAAAAACGTTACGTTTG‑AAGGTCTTCTGTAACAATGATGAc > 1:150157/1‑90 (MQ=255)
tGGGTAAAACCTGAAGATCTGGTGCATTATGATTTGAATGTCGCCACCCGAAAAACGTTACGTTTG‑AAGGTCTTCTGTAACAATGATGAc > 1:170550/1‑90 (MQ=255)
gggTAAAACCTGAAGATCTGGTGCATTATGATTTGAATGTCGCCACCCGAAAAACGTTACGTTTG‑AAGGTCTTCTGTAACAATGATGACa < 1:59110/90‑1 (MQ=255)
gggTAAAACCTGAAGATCTGGTGCATTATGATTTGAATGTCGCCACCCGAAAAACGTTACGTTTG‑AAGGTCTTCTGTAACAATGATGACa < 2:272286/90‑1 (MQ=255)
gTAAAACCTGAAGATCTGGTGCATTATGATTTGAATGTCGCCACCCGAAAAACGTTACGTTTGAAAGGTCTTCTGTAACAATGATGACAg < 2:531011/90‑1 (MQ=255)
aaaCCTGAAGATCTGGTGCATTATGATTTGAATGTCGCCACCCGAAAAACGTTACGTTTG‑AAGGTCTTCTGTAACAATGATGACAGCCAt > 2:273133/1‑90 (MQ=255)
tCTGGTGCATTATGATTTGAATGTCGCCACCCGAAAAACGTTACGTTTGAAAGGTCTTCTGTAACAATGATGACAGCCATTACTGGCTGt > 2:14055/1‑90 (MQ=255)
tGGTGCATTATGATTTGAATGTCGCCACCCGAAAAACGTTACGTTTG‑AAGGTCTTCTGTAACAATGATGACAGCCATTACTGGCTGTCAg > 1:408419/1‑90 (MQ=255)
aTTATGATTTGAATGTCGCCACCCGAAAAACGTTACGTTTG‑AAGGTCTTCTGTAACAATGATGACAGCCATTACTGGCTGTCAGATTGaa > 2:568393/1‑90 (MQ=255)
gATTTGAATGTCGCCACCCGAAAAACGTTACGTTTG‑AAGGTCTTCTGTAACAATGATTACAGCCATTACTGGCTGTCAGATTGAAAAttt > 2:420132/1‑90 (MQ=255)
ttGAATGTCGCCACCCGAAAAACGTTACGTTTG‑AAGGTCTTCTGTAACAATGATGACAGCCATTACTGGCTGTCAGATTGAAAATTTAGt > 2:306547/1‑90 (MQ=255)
cGAAAAACGTTACGTTTG‑AAGGTCTTCTGTAACAATGATGACAGCCATTACTGGCTGTCAGATTGAAAATTTAGTGGTTAACGAATTccc < 1:369689/90‑1 (MQ=255)
gttacgttTG‑AAGGTCTTCTGTAACAATGATGACAGc < 2:192645/37‑1 (MQ=38)
gttacgttTG‑AAGGTCTTCTGTAACAATGATGACAGc > 1:192645/1‑37 (MQ=38)
|
AAGAGTTTCAGGACTACGCGTGGGTAAAACCTGAAGATCTGGTGCATTATGATTTGAATGTCGCCACCCGAAAAACGTTACGTTTGAAAGGTCTTCTGTAACAATGATGACAGCCATTACTGGCTGTCAGATTGAAAATTTAGTGGTTAACGAATTCCC > NZ_CP009273/2358358‑2358516
|
| Alignment Legend |
|---|
Aligned base mismatch/match (shaded by quality score): ATCG/ATCG < 3 ≤ ATCG/ATCG < 28 ≤ ATCG/ATCG < 34 ≤ 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
AAGAGTTTCAGGACTACGCGTGGGTAAAACCTGAAGATCTGGTGCATTATGATTTGAATGTCGCCACCCGAAAAACGTTACGTTTGAAAGGTCTTCTGTAACAATGATGACAGCCATTACTGGCTGTCAGATTGAAAATTTAGTGGTTAACGAATTCCCCATCCAGATAAACTTTGCCTTTT > NZ_CP009273/2358358‑2358539
|
AAGAGTTTCAGGACTACGCGTGGGTAAAACCTGAAGATCTGGTGCATTATGATTTGAATGTCGCCACCCGAAAAACGTTACGTTTG‑AAGGTCTTCTGTAA < SRR3722111.172311/100‑1 (MQ=60)
TTTCAGGACTACGCGTGGGTAAAACCTGAAGATCTGGTGCATTATGATTTGAATGTCGCCACCCGAAAAACGTTACGTTTG‑AAGGTCTTCTGTAACAATG > SRR3722111.275632/1‑100 (MQ=60)
TTTCAGGACTACGCGTGGGTAAAACCTGAAGATCTGGTGCATTATGATTTGAATGTCGCCACCCGAAAAACGTTACGTTTG‑AAGGTCTTCTGTAACAATG > SRR3722111.391788/1‑100 (MQ=60)
TTTCAGGACTACGCGTGGGTAAAACCTGAAGATCTGGTGCATTATGATTTGAATGTCGCCACCCGAAAAACGTTACGTTTG‑AAGGTCTTCTGTAACAATG > SRR3722111.508044/1‑100 (MQ=60)
GGACTACGCGTGGGTAAAACCTGAAGATCTGGTGCATTATGATTTGAATGTCGCCACCCGAAAAACGTTACGTTTG‑AAGGTCTTCTGTAACAATGATGAC > SRR3722111.152041/1‑100 (MQ=60)
GGACTACGCGTGGGTAAAACCTGAAGATCTGGTGCATTATGATTTGAATGTCGCCACCCGAAAAACGTTACGTTTG‑AAGGTCTTCTGTAACAATGATGAC > SRR3722111.172682/1‑100 (MQ=60)
GTGGGTAAAACCTGAAGATCTGGTGCATTATGATTTGAATGTCGCCACCCGAAAAACGTTACGTTTG‑AAGGTCTTCTGTAACAATGATGACAGCCATTAC < SRR3722111.458608/100‑1 (MQ=60)
GGGTAAAACCTGAAGATCTGGTGCATTATGATTTGAATGTCGCCACCCGAAAAACGTTACGTTTG‑AAGGTCTTCTGTAACAATGATGACAGCCATTACTG < SRR3722111.59816/100‑1 (MQ=60)
CCTGAAGATCTGGTGCATTATGATTTGAATGTCGCCACCCGAAAAACGTTACGTTTG‑AAGGTCTTCTGTAACAATGATGACAGCCATTACTGGCTGTCAG > SRR3722111.414402/1‑100 (MQ=60)
CCCGAAAAACGTTACGTTTG‑AAGGTCTTCTGTAACAATGATGACAGCCATTACTGGCctgtctcttatacacatctgacgctgccgacgaatgtcaatgt > SRR3722111.195050/1‑57 (MQ=60)
CGAAAAACGTTACGTTTG‑AAGGTCTTCTGTAACAATGATGACAGCCATTACTGGCTGTCAGATTGAAAATTTAGTGGTTAACGAATTCCCCATCCAGATA < SRR3722111.374919/100‑1 (MQ=60)
GTTTG‑AAGGTCTTCTGTAACAATGATGACAGCCATTACTGGCTGTCAGATTGAAAATTTAGTGGTTAACGAATTCCCCATCCAGATAAACTTTGCCTTTT > SRR3722111.526298/1‑100 (MQ=60)
|
AAGAGTTTCAGGACTACGCGTGGGTAAAACCTGAAGATCTGGTGCATTATGATTTGAATGTCGCCACCCGAAAAACGTTACGTTTGAAAGGTCTTCTGTAACAATGATGACAGCCATTACTGGCTGTCAGATTGAAAATTTAGTGGTTAACGAATTCCCCATCCAGATAAACTTTGCCTTTT > NZ_CP009273/2358358‑2358539
|
| Alignment Legend |
|---|
Aligned base mismatch/match (shaded by quality score): ATCG/ATCG < 0 ≤ ATCG/ATCG < 27 ≤ ATCG/ATCG < 32 ≤ ATCG/ATCG < 35 ≤ ATCG/ATCG < 41 ≤ ATCG/ATCG |
Unaligned base: atcg Masked matching base: atcg Alignment gap: ‑ Deleted base: ‑ |
