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 |
3,934,995 |
+C |
intergenic (‑308/‑173) |
yieP ← / → BW25113_RS19520 |
FadR/GntR family transcriptional regulator/16S ribosomal RNA |
|
| |
seq id |
position |
ref |
new |
freq |
score (cons/poly) |
reads |
annotation |
genes |
product |
| * | NZ_CP009273 | 3,934,991 | 1 | . | C | 96.3%
| 77.7
/ ‑2.8
| 27 | intergenic (‑304/‑177) | yieP/BW25113_RS19520 | FadR/GntR family transcriptional regulator/16S ribosomal RNA |
| Reads supporting (aligned to +/- strand): ref base . (1/0); new base C (11/15); total (12/15) |
| Fisher's exact test for biased strand distribution p-value = 4.44e-01 |
| Kolmogorov-Smirnov test that lower quality scores support variant p-value = 3.20e-01 |
GGGGTTCTCCTGAGAACTCCGGCAGAGAAAGCAAAAATAAATGCTTGACTCTGTAGCGGGAAAGCGTATTATGCACA‑CCCCGCGCCGCTGAGAAAAAGCAAAGCGGCACTGCTCTTTAACAATTTATCAGACAATCTGTGTGGGCACTCGAAGATACG > NZ_CP009273/3934915‑3935072
|
ggggTTCTCCTGAGAACTCCGGCAGAGAAAGCAAAAATAAATGCTTGACTCTGTAGCGGGAAAGCGTATTATGCACACCCCCGCGCCGCt < 1:151829/90‑1 (MQ=255)
tctcCTGAGAACTCCGGCAGAGAAAGCAAAAATAAATGCTTGACTCTGTAGCGGGAAAGCGTATTATGCACACCCCCGCGCCGCTGAGaa < 1:146958/90‑1 (MQ=255)
tGAGAACTCCGGCAGAGAAAGCAAAAATAAATGCTTGACTCTGTAGCGGGAAAGCGTATTATGCACACCCCCGCGCCGCTGAGAAaaagc < 2:171052/90‑1 (MQ=255)
gagaACTCCGGCAGAGAAAGCAAAAATAAATGCTTGACTCTGTAGCGGGAAAGCGTATTATGCACACCCCCGCGCCGCTGAGAAaaagca > 1:116206/1‑90 (MQ=255)
gaACTCCGGCAGAGAAAGCAAAAATAAATGCTTGACTCTGTAGCGGGAAAGCGTATTATGCACACCCCCGCGCCGCTGAGAAaaagcaaa > 2:372074/1‑90 (MQ=255)
gaACTCCGGCAGAGAAAGCAAAAATAAATGCTTGACTCTGTAGCGGGAAAGCGTATTATGCACACCCCCGCGCCGCTGAGAAaaagcaaa > 2:309758/1‑90 (MQ=255)
ccGGCAGAGAAAGCAAAAATAAATGCTTGACTCTGTAGCGGGAAAGCGTATTATGCACACCCCCGCGCCGCt < 1:190400/72‑1 (MQ=255)
ccGGCAGAGAAAGCAAAAATAAATGCTTGACTCTGTAGCGGGAAAGCGTATTATGCACACCCCCGCGCCGCt > 2:190400/1‑72 (MQ=255)
gCAGAGAAAGCAAAAATAAATGCTTGACTCTGTAGCGGGAAAGCGTATTATGCACACCCCCGCGCCGCTGAGAAAAAGCAAAGCGGCACt < 2:52962/90‑1 (MQ=255)
agagAAAGCAAAAATAAATGCTTGACTCTGTAGCGGGAAAGCGTATTATGCACACCCCCGCGCCGCTGAGAAAAAGCAAAGCGGCACTGc < 1:189044/90‑1 (MQ=255)
agagAAAGCAAAAATAAATGCTTGACTCTGTAGCGGGAAAGCGTATTATGCACACCCCCGCGCCGCTGAGAAAAAGCAAAGCGGCACTGc < 1:396573/90‑1 (MQ=255)
agagAAAGCAAAAATAAATGCTTGACTCTGTAGCGGGAAAGCGTATTATGCACACCCCCGCGCCGCTGAGAAAAAGCAAAGCGGCACTGc < 2:450127/90‑1 (MQ=255)
aGCAAAAATAAATGCTTGACTCTGTAGCGGGAAAGCGTATTATGCACACCCCCGCGCCGCTGAGAAAAAGCAAAGCGGCACTGCTCTTTa < 2:434996/90‑1 (MQ=255)
cAAAAATAAATGCTTGACTCTGTAGCGGGAAAGCGTATTATGCACACCCCCGCGCCGCTGAGAAAAAGCAAAGCGGCACTGCTCTTTAAc > 2:364991/1‑90 (MQ=255)
cAAAAATAAATGCTTGACTCTGTAGCGGGAAAGCGTATTATGCACACCCCCGCGCCGCTGAGAAAAAGCAAAGCGGCACTGCTCTTTAAc < 2:438692/90‑1 (MQ=255)
aaaaTAAATGCTTGACTCTGTAGCGGGAAAGCGTATTATGCACACCCCCGCGCCGCTGAGAAAAAGCAAAGCGGCACTGCTCTTTAACaa < 1:434547/90‑1 (MQ=255)
aaaaTAAATGCTTGACTCTGTAGCGGGAAAGCGTATTATGCACACCCCCGCGCCGCTGAGAAAAAGCAAAGCGGCACTGCTCTTTAACaa < 2:506330/90‑1 (MQ=255)
aaaaTAAATGCTTGACTCTGTAGCGGGAAAGCGTATTATGCACACCCCCGCGCCGCTGAGAAAAAGCAAAGCGGCACTGCTCTTTAACaa < 2:288931/90‑1 (MQ=255)
tGACTCTGTAGCGGGAAAGCGTATTATGCACACCCCCGCGCCGCTGAGAAAAAGCAAAGCGGCACTGCTCTTTAACAATTTATCAGACaa > 2:173073/1‑90 (MQ=255)
ctGTAGCGGGAAAGCGTATTATGCACACCCCCGCGCCGCTGAGAAAAAGCAAAGCGGCACTGCTCTTTAACAATTTATCAGACAATCtgt > 2:417593/1‑90 (MQ=255)
ctGTAGCGGGAAAGCGTATTATGCACA‑CCCCGCGCCGCTGAGAAAAAGCAAAGCGGCACTGCTCTTTAACAATTTATCAGACAATCtgtg > 1:303789/1‑90 (MQ=39)
gCGGGAAAGCGTATTATGCACACCCCCGCGCCGCTGAGAAAAAGCAAAGCGGCACTGCTCTTTAACAATTTATCAGACAATCTGTGTggg > 2:103769/1‑90 (MQ=255)
gggAAAGCGTATTATGCACACCCCCGCGCCGCTGAGAAAAAGCAAAGCGGCACt > 1:479689/1‑54 (MQ=14)
gggAAAGCGTATTATGCACACCCCCGCGCCGCTGAGAAAAAGCAAAGCGGCACt < 2:479689/54‑1 (MQ=14)
gggAAAGCGTATTATGCACACCCCCGCGCCGCTGAGAAAAAGCAAAGCGGCACTGCTCTTTAACAATTTATCAGACAATCTGTGTGGGCa > 1:323376/1‑90 (MQ=255)
gggAAAGCGTATTATGCACACCCCCGCGCCGCTGAGAAAAAGCAAAGCGGCACTGCTCTTTAACAATTTATCAGACAATCTGTGTGGGCa > 2:183883/1‑90 (MQ=255)
tatGCACACCCCCGCGCCGCTGAGAAAAAGCAAAGCGGCACTGCTCTTTAACAATTTATCAGACAATCTGTGTGGGCACTCGAAGATACg < 2:40361/90‑1 (MQ=255)
|
GGGGTTCTCCTGAGAACTCCGGCAGAGAAAGCAAAAATAAATGCTTGACTCTGTAGCGGGAAAGCGTATTATGCACA‑CCCCGCGCCGCTGAGAAAAAGCAAAGCGGCACTGCTCTTTAACAATTTATCAGACAATCTGTGTGGGCACTCGAAGATACG > NZ_CP009273/3934915‑3935072
|
| Alignment Legend |
|---|
Aligned base mismatch/match (shaded by quality score): ATCG/ATCG < 3 ≤ ATCG/ATCG < 31 ≤ ATCG/ATCG < 35 ≤ ATCG/ATCG < 36 ≤ ATCG/ATCG < 41 ≤ ATCG/ATCG |
Unaligned base: atcg Masked matching base: atcg Alignment gap: ‑ Deleted base: ‑ |
GATK/CNVnator alignment
BRESEQ :: bam2aln output
GGGGTTCTCCTGAGAACTCCGGCAGAGAAAGCAAAAATAAATGCTTGACTCTGTAGCGGGAAAGCGTATTATGCACA‑CCCCGCGCCGCTGAGAAAAAGCAAAGCGGCACTGCTCTTTAACAATTTATCAGACAATCTGTGTGGGCACTCGAAGATACGGATTCTTAACGTCGCAAG > NZ_CP009273/3934915‑3935090
|
agagacagCCTGAGAACTCCGGCAGAGAAAGCAAAAATAAATGCTTGACTCTGTAGCGGGAAAGCGTATTATGCACACCCCCGCGCCGCTGAGAAAAAGC < SRR3722111.192781/92‑1 (MQ=7)
GGGGTTCTCCTGAGAACTCCGGCAGAGAAAGCAAAAATAAATGCTTGACTCTGTAGCGGGAAAGCGTATTATGCACACCCCCGCGCCGCTGAGAAAAAGC < SRR3722111.153735/100‑1 (MQ=7)
GGGTTCTCCTGAGAACTCCGGCAGAGAAAGCAAAAATAAATGCTTGACTCTGTAGCGGGAAAGCGTATTATGCACACCCCCGCGCCGCTGAGAAAAAGCA > SRR3722111.117672/1‑100 (MQ=9)
TCTCCTGAGAACTCCGGCAGAGAAAGCAAAAATAAATGCTTGACTCTGTAGCGGGAAAGCGTATTATGCACACCCCCGCGCCGCTGAGAAAAAGCAAAGC < SRR3722111.148809/100‑1 (MQ=24)
AGAGAAAGCAAAAATAAATGCTTGACTCTGTAGCGGGAAAGCGTATTATGCACACCCCCGCGCCGCTGAGAAAAAGCAAAGCGGCACTGCTCTTTAACAA < SRR3722111.191402/100‑1 (MQ=24)
AGAGAAAGCAAAAATAAATGCTTGACTCTGTAGCGGGAAAGCGTATTATGCACACCCCCGCGCCGCTGAGAAAAAGCAAAGCGGCACTGCTCTTTAACAA < SRR3722111.402325/100‑1 (MQ=24)
AAAATAAATGCTTGACTCTGTAGCGGGAAAGCGTATTATGCACACCCCCGCGCCGCTGAGAAAAAGCAAAGCGGCACTGCTCTTTAACAATTTATCAGAC < SRR3722111.441045/100‑1 (MQ=24)
ATGCTTGACTCTGTAGCGGGAAAGCGTATTATGCACA‑CCCCGCGCCGCTGAGAAAAAGCAAAGCGGCACTGCTCTTTAACAATTTATCAGACAATCTGTG > SRR3722111.307725/1‑100 (MQ=26)
ACTCTGTAGCGGGAAAGCGTATTATGCACACCCCCGCGCCGCTGAGAAAAAGCAAAGCGGCACTGCTCTTTAACctgtctcttatacacatctgacgctg > SRR3722111.487037/1‑74 (MQ=27)
ACTCTGTAGCGGGAAAGCGTATTATGCACACCCCCGCGCCGCTGAGAAAAAGCAAAGCGGCACTGCTCTTTAACAATTTATCAGACAATCTGTGTGGGCA > SRR3722111.327680/1‑100 (MQ=24)
C‑CCCCGCGCCGCTGAGAAAAAGCAAAGCGGCACTGCTCTTTAACAATTTATCAGACAATCTGTGTGGGCACTCGAAGATACGGATTCTTAACGTCGCAAG > SRR3722111.258220/1‑100 (MQ=7)
C‑CCCCGCGCCGCTGAGAAAAAGCAAAGCGGCACTGCTCTTTAACAATTTATCAGACAATCTGTGTGGGCACTCGAAGATACGGATTCTTAACGTCGCAAG > SRR3722111.470271/1‑100 (MQ=7)
|
GGGGTTCTCCTGAGAACTCCGGCAGAGAAAGCAAAAATAAATGCTTGACTCTGTAGCGGGAAAGCGTATTATGCACA‑CCCCGCGCCGCTGAGAAAAAGCAAAGCGGCACTGCTCTTTAACAATTTATCAGACAATCTGTGTGGGCACTCGAAGATACGGATTCTTAACGTCGCAAG > NZ_CP009273/3934915‑3935090
|
| Alignment Legend |
|---|
Aligned base mismatch/match (shaded by quality score): ATCG/ATCG < 0 ≤ ATCG/ATCG < 33 ≤ ATCG/ATCG < 34 ≤ ATCG/ATCG < 35 ≤ ATCG/ATCG < 41 ≤ ATCG/ATCG |
Unaligned base: atcg Masked matching base: atcg Alignment gap: ‑ Deleted base: ‑ |
