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 F3 I157 R1
|
5 |
22.3 |
1326252 |
93.5% |
1240045 |
82.9 |
Breseq alignment
BRESEQ :: Evidence
|
| evidence |
seq id |
position |
mutation |
annotation |
gene |
description |
| RA |
NZ_CP009273 |
4,372,536 |
T→A |
I26N (ATC→AAC) |
epmA → |
elongation factor P‑‑(R)‑beta‑lysine ligase |
|
| |
seq id |
position |
ref |
new |
freq |
score (cons/poly) |
reads |
annotation |
genes |
product |
| * | NZ_CP009273 | 4,372,536 | 0 | T | A | 81.8%
| 51.8
/ 4.2
| 22 | I26N (ATC→AAC) | epmA | elongation factor P‑‑(R)‑beta‑lysine ligase |
| Reads supporting (aligned to +/- strand): ref base T (2/2); new base A (9/9); total (11/11) |
| 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 |
TGAGCGAAACGGCATCCTGGCAGCCGAGCGCATCCATTCCTAACTTATTAAAACGCGCGGCGATTATGGCGGAGATCCGTCGTTTCTTTGCCGATCGTGGAGTGCTGGAGGTGGAGACGCCTTGTATGAGCCAGGCGACGGTAACCGATATTCATTTGGTCC > NZ_CP009273/4372461‑4372622
|
tGAGCGAAACGGCATCCTGGCAGCCGAGCGCATCCATTCCTAACTTATTAAAACGCGCGGCGATTATGGCGGAGATCCGTCGTTTCTTTg > 1:300264/1‑90 (MQ=255)
tGAGCGAAACGGCATCCTGGCAGCCGAGCGCATCCATTCCTAACTTATTAAAACGCGCGGCGATTATGGCGGAAAAACGCGGTTTCtttt > 2:69459/1‑89 (MQ=255)
ggCATCCTGGCAGCCGAGCGCATCCATTCCTAACTTATTAAAACGCGCGGCGATTATGGCGGAGAACCGTCGTTTCTTTGCCGATCGTgg < 1:624548/90‑1 (MQ=255)
tGGCAGCCGAGCGCATCCATTCCTAACTTATTAAAACGCGCGGCGATTATGGCGGAGAACCGTCGTTTCTTTGCCGATCGTGGAGTGCTg < 2:177261/90‑1 (MQ=255)
aTCCATTCCTAACTTATTAAAACGCGCGGCGATTATGGCGGAGAACCGTCGTTTCTTTGCCGATCGTGGAGTGCTGGAGGTGGAGACGcc < 2:399521/90‑1 (MQ=255)
tacATTCCTAACATACAAAAACGAGCGGCGATTATGGCGCAGAACCGTTGTTTCTTTGCAAATCGTGGAGTGCTGGAGGTGGAGACGCCt < 2:318914/88‑1 (MQ=255)
tCCATTCCTAACTTATTAAAACGCGCGGCGATTATGGCGGAGATCCGTCGTTTCTTTGCCGATCGTGGAGTGCTGGAGGTGGAGACGCCt < 2:95373/90‑1 (MQ=255)
tCCATTCCTAACTTATTAAAACGCGCGGCGATTATGGCGGAGAACCGTCGTTTCTTTGCCGATCGTGGAGTGCTGGAGGTGGAGACGCCt < 1:213266/90‑1 (MQ=255)
aTTCCTAACTTATTAAAACGCGCGGCGATTATGGCGGAGAACCGTCGTTTCTTTGCCGATCGTGGAGTGCTGGAGGTGGAGACGCCTTGt > 1:107288/1‑90 (MQ=255)
ttCCTAACTTATTAAAACGCGCGGCGATTATGGCGGAGAACCGTCGTTTCTTTGCCGATCGTg > 1:317735/1‑63 (MQ=255)
ttCCTAACTTATTAAAACGCGCGGCGATTATGGCGGAGAACCGTCGTTTCTTTGCCGATCGTg < 2:317735/63‑1 (MQ=255)
tattaAAACGCGCGGCGATTATGGCGGAGAACCGTCGTTTCTTTGCCGATCGTgg > 1:524189/1‑55 (MQ=255)
tattaAAACGCGCGGCGATTATGGCGGAGAACCGTCGTTTCTTTGCCGATCGTgg < 2:524189/55‑1 (MQ=255)
attaAAACGCGCGGCGATTATGGCGGAGAACCGTCGTTTCTTTGCCGATCGTGGAGTGCTGGAGGGGGAGACGCCTTGTATGAGCCAGGc > 1:594538/1‑90 (MQ=255)
taAAACGCGCGGCGATTATGGCGGAGAACCGTCGTTTCTTTTCCGATCGTGGAGGGCTGGGGGGGGGGACGCCTTGTATGAGCCAGGCGa > 2:181159/1‑90 (MQ=255)
taAAACGCGCGGCGATTATGGCGGAGAACCGTCGTTTCTTTTCCGATCGTGGAGGGCTGGAGGGGGGGACGCCTTGTATGAGCCAGGCGa > 2:178064/1‑90 (MQ=255)
cgcgcgGCGATTATGGCGGAGATCCGTCGTTTCTTTGCCGATCGTgggg > 2:327426/1‑47 (MQ=255)
cgcgcgGCGATTATGGCGGAGATCCGTCGTTTCTTTGCCGATCGTGGAg < 1:327426/49‑1 (MQ=255)
cgcgcgGCGATTATGGCGGAGAACCGTCGTTTCTTTGCCGATCGTGGAGTGCTGGAGGt < 1:619403/59‑1 (MQ=255)
cgcgcgGCGATTATGGCGGAGAACCGTCGTTTCTTTGCCGATCGTGGAGTGCTGGAGGt > 2:619403/1‑59 (MQ=255)
ggcgATTATGGCGGAGAACCGTCGTTTCTTTGCCGATCGTGGAGTGCTGGAGGTGGAGACGCCTTGTATGAGCCAGGCGACGGTAACCGa < 1:181159/90‑1 (MQ=255)
agaACCGTCGTTTCTTTGCCGATCGTGGAGTGCTGGAGGTGGAGACGCCTTGTATGAGCCAGGCGACGGTAACCGATATTCATTTGGTcc > 1:100049/1‑90 (MQ=255)
|
TGAGCGAAACGGCATCCTGGCAGCCGAGCGCATCCATTCCTAACTTATTAAAACGCGCGGCGATTATGGCGGAGATCCGTCGTTTCTTTGCCGATCGTGGAGTGCTGGAGGTGGAGACGCCTTGTATGAGCCAGGCGACGGTAACCGATATTCATTTGGTCC > NZ_CP009273/4372461‑4372622
|
| Alignment Legend |
|---|
Aligned base mismatch/match (shaded by quality score): ATCG/ATCG < 3 ≤ ATCG/ATCG < 8 ≤ ATCG/ATCG < 19 ≤ ATCG/ATCG < 33 ≤ ATCG/ATCG < 41 ≤ ATCG/ATCG |
Unaligned base: atcg Masked matching base: atcg Alignment gap: ‑ Deleted base: ‑ |
GATK/CNVnator alignment
BRESEQ :: bam2aln output
AAAAACTGGAGATTTAACTATGAGCGAAACGGCATCCTGGCAGCCGAGCGCATCCATTCCTAACTTATTAAAACGCGCGGCGATTATGGCGGAGATCCGTCGTTTCTTTGCCGATCGTGGAGTGCTGGAGGTGGAGACGCCTTGTATGAGCCAGGCGACGGTAACCGATATTCATTTGGTCCCGTTTGAG > NZ_CP009273/4372441‑4372630
|
AAAAACTGGAGATTTAACTATGAGCGAAACGGCATCCTGGCAGCCGAGCGCATCCATTCCTAACTTATTAAAACGCGCGGCGATTATGGCGGAGAACCGT < SRR3722027.597107/100‑1 (MQ=60)
GATTTAACTATGAGCGAAACGGCATCCTGGCAGCCGAGCGCATCCATTCCTAACTTATTAAAACGCGCGGCGATTATGGCGGAGATCCGTCGTTTCTTTG > SRR3722027.305627/1‑100 (MQ=60)
GGCATCCTGGCAGCCGAGCGCATCCATTCCTAACTTATTAAAACGCGCGGCGATTATGGCGGAGAACCGTCGTTTCTTTGCCGATCGTGGAGTGCTGGAG < SRR3722027.637359/100‑1 (MQ=60)
tcgtgggctcggagatgtgtataagagacagCTTATTAAAACGCGCGGCGATTATGGCGGAGATCCGTCGTTTCTTTGCCGATCGTGGAGTGCTGGAGGT < SRR3722027.333383/69‑1 (MQ=60)
ggagatgtgtataagagacagCTTATTAAAACGCGCGGCGATTATGGCGGAGAACCGTCGTTTCTTTGCCGATCGTGGAGTGCTGGAGGTGGAGACGCCT < SRR3722027.632111/79‑1 (MQ=60)
GAGCGCATCCATTCCTAACTTATTAAAACGCGCGGCGATTATGGCGGAGAACCGTCGTTTCTTTGCCGATCGTGGAGTGCTGGAGGTGGAGACGCCTTGT > SRR3722027.109187/1‑100 (MQ=60)
AGCGCATCCATTCCTAACTTATTAAAACGCGCGGCGATTATGGCGGAGAACCGTCGTTTCTTTGCCGATCGTGGAGTGCTGGActgtctcttatacacat > SRR3722027.323509/1‑83 (MQ=60)
TCCATTCCTAACTTATTAAAACGCGCGGCGATTATGGCGGAGAACCGTCGTTTCTTTGCCGATCGTGGAGTGCTGGAGGTGGAGACGCCTTGTATGAGCC < SRR3722027.216949/100‑1 (MQ=60)
ATTCCTAACTTATTAAAACGCGCGGCGATTATGGCGGAGAACCGTCGTTTCTTTGCCGATCGTGGAGTGCTGGAGctgtctcttatacacatctccgagc > SRR3722027.534797/1‑75 (MQ=60)
TTCCTAACTTATTAAAACGCGCGGCGATTATGGCGGAGAACCGTCGTTTCTTTGCCGATCGTGGAGTGCTGGAGGGGGAGACGCCTTGTATGAGCCAGGC > SRR3722027.606724/1‑100 (MQ=60)
GGCGATTATGGCGGAGAACCGTCGTTTCTTTGCCGATCGTGGAGTGCTGGAGGTGGAGACGCCTTGTATGAGCCAGGCGACGGTAACCGATATTCATTTG < SRR3722027.184333/100‑1 (MQ=60)
GTTATGGCGGAGAACCGTCGTTTCTTTGCCGATCGTGGAGTGCTGGAGGTGGAGACGCCTTGTATGAGCCAGGCGACGGTAACCGATATTCATTTGGTCC < SRR3722027.179521/100‑1 (MQ=60)
ATTATGGCGGAGAACCGTCGTTTCTTTGCCGATCGTGGAGTGCTGGAGGTGGAGACGCCTTGTATGAGCCAGGCGACGGTAACCGATATTCATTTGGTCC > SRR3722027.101823/1‑100 (MQ=60)
GGAGAACCGTCGTTTCTTTGCCGATCGTGGAGTGCTGGAGGTGGAGACGCCTTGTATGAGCCAGGCGACGGTAACCGATATTCATTTGGTCCCGTTTGAG > SRR3722027.517470/1‑100 (MQ=60)
|
AAAAACTGGAGATTTAACTATGAGCGAAACGGCATCCTGGCAGCCGAGCGCATCCATTCCTAACTTATTAAAACGCGCGGCGATTATGGCGGAGATCCGTCGTTTCTTTGCCGATCGTGGAGTGCTGGAGGTGGAGACGCCTTGTATGAGCCAGGCGACGGTAACCGATATTCATTTGGTCCCGTTTGAG > NZ_CP009273/4372441‑4372630
|
| Alignment Legend |
|---|
Aligned base mismatch/match (shaded by quality score): ATCG/ATCG < 0 ≤ ATCG/ATCG < 19 ≤ ATCG/ATCG < 29 ≤ ATCG/ATCG < 35 ≤ ATCG/ATCG < 41 ≤ ATCG/ATCG |
Unaligned base: atcg Masked matching base: atcg Alignment gap: ‑ Deleted base: ‑ |
