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 |
|
A23 F171 I0 R2
|
49 |
45.2 |
1012374 |
92.5% |
936445 |
139.6 |
Breseq alignment
BRESEQ :: Evidence
|
| evidence |
seq id |
position |
mutation |
freq |
annotation |
gene |
description |
| RA |
CP000730 |
2,455,692 |
Δ1 bp |
100% |
coding (1210/1260 nt) |
USA300HOU_2315 → |
hypothetical membrane protein |
|
| |
seq id |
position |
ref |
new |
freq |
score (cons/poly) |
reads |
annotation |
genes |
product |
| * | CP000730 | 2,455,692 | 0 | G | . | 97.1%
| 150.4
/ ‑2.7
| 34 | coding (1210/1260 nt) | USA300HOU_2315 | hypothetical membrane protein |
| Reads supporting (aligned to +/- strand): ref base G (0/0); major base . (18/15); minor base A (1/0); total (19/15) |
| Fisher's exact test for biased strand distribution p-value = 1.00e+00 |
| Kolmogorov-Smirnov test that lower quality scores support variant p-value = 9.98e-01 |
| Rejected as polymorphism: E-value score below prediction cutoff. |
| Rejected as polymorphism: Frequency below/above cutoff threshold. |
| Rejected as polymorphism: Variant not supported by required number of reads on each strand. |
| Rejected as polymorphism: Polymorphic indel expands or contracts a homopolymer stretch. |
AGCAGAATCAGTTAAACAAGCACCACAAAGTGACGATTTAACAAACGATTCAAATGAAGATGAAATAGAGCAATCATTAAAAGAACCTGCGACTTATAAAGAAGACAGACGTTCATCAGTTGTAATTGATGCAGAAAAACAT‑ATCGAAAAAACTGAAGAACAATCTTCAGATAAAAACAAATAATAACAAAGCGCTTGCTAGTACCTCTTAAAAAGATGATGCTAGCAAGCGCTTTTCTATACTATATATTATTTTTCTAAAATTT > CP000730/2455559‑2455824
|
agcagAATCAGTTAAACAAGCACCACAAAGTGACGATTTAACAAACGATTCAAATGAAGATGAAATAGAGCAATCATTAAAAGAACCTGCGACTTATAAAGAAGACAGACGTTCATCAGTTGTAATTGATGCAaaaaaatt > 1:300412/1‑139 (MQ=255)
agcagAATCAGTTAAACAAGCACCACAAAGTGACGATTTAACAAACGATTCAAATGAAGATGAAATAGAGCAATCATTAAAAGAACCTGCGACTTATAAAGAAGACAGACGTTCATCAGTTGTAATTGATGCAaaaaaatt > 2:16317/1‑139 (MQ=255)
agAATCAGTTAAACAAGCACCACAAAGTGACGATTTAACAAACGATTCAAATGAAGATGAAATAGAGCAATCATTAAAAGAACCTGCGACTTATAAAGAAGACAGACGTTCATCAGTTGTAATTGATGCAaaaaaattatc < 2:491047/141‑6 (MQ=255)
aaTCAGTTAAACAAGCACCACAAAGTGACGATTTAACAAACGATTCAAATGAAGATGAAATAGAGCAATCATTAAAAGAACCTGCGACTTATAAAGAAGACAGACGTTCATCAGTTGTAATTGATGCAaaaaaattatcga > 1:15397/1‑134 (MQ=255)
aTCAGTTAAACAAGCACCACAAAGTGACTATTTAACAAACGATTCAAATAAAGATGAAATAGAGCAATCATTAAAAGAACCTGCGACTTATAAAGAAGACAGACGTTCATCAGTTGTAATTGATGCAaaaaaattatcgaa < 2:216262/141‑9 (MQ=255)
aGTTAAACAAGCACCACAAAGTGACGATTTAACAAACGATTCAAATGAAGATGAAATAGAGCAATCATTAAAAGAACCTGCGACTTATAAAGAAGACAGACGTTCATCAGTTGTAATTGATGCA‑AAAAAATT‑ATCGaaaaa > 2:302098/1‑141 (MQ=255)
gTTAAACAAGCACCACAAAGTGACGATTTAACAAACGATTCAAATGAAGATGAAATAGAGCAATCATTAAAAGAACCTGCGACTTATAAAGAAGACAGACGTTCATCAGTTGTAATTGATGCA‑AAAAAATT‑ATCGaaaaaa > 2:292180/1‑141 (MQ=255)
ttcaaCAAGCACCACAAAGTGACGATTTAACAAACGATTCAAATGAAGATGAAATAGAGCAATCATTAAAAGAACCTGCGACTTATAAAGAAGACAGACGTTCATCAGTTGTAATTGATGCA‑AAAAAATT‑ATCGAAAAAAc < 2:433680/138‑1 (MQ=255)
ttAAACAAGCACCACAAAGTGACGATTTAACAAACGATTCAAATGAAGATGAAATAGAGCAATCATTAAAAGAACCTGCGACTTATAAAGAAGACAGACGTTCCTCAGTTGTAATTGATGCA‑AACAAATT‑ATCGAAAAAAc > 2:17090/1‑141 (MQ=255)
cAAGCACCACAAAGTGACGATTTAACAAACGATTCAAATGAAGATGAAATAGAGCAATCATTAAAAGAACCTGCGACTTATAAAGAAGACAGACGTTCGTCAGTTGTGGTTGCTGC‑‑AACAACATAATCGAAAAAACTgaag > 1:18171/1‑141 (MQ=255)
cAAGCACCACAAAGTGACGATTTAACAAACGATTCAAATGAAGATGAAATAGAGCAATCATTAAAAGAACCTGCGACTTATAAAGAAGACAGACGTTCATCAGTTGTAATTGATGCA‑AAAAAATT‑ATCGAAAAAACTgaag < 1:495325/141‑1 (MQ=255)
gCACCACAAAGTGACGATTTAACAAACGATTCAAATGAAGATGAAATAGAGCAATCATTAAAAGAACCTGCGACTTATAAAGAAGACAGACGTTCATCAGTTGTAATTGATGCA‑AAAAAATT‑ATCGAAAAAACTGAAGAAc > 1:335463/1‑141 (MQ=255)
gCACCACAAAGTGACGACTTAACAAACGATACAAATGAAGATGAAAGAGAGCACTCATTAAAAGAACCTACGACATATAAAGAATACAGACGATCATCAGTTGTAATTGATGCA‑AAAAAATT‑ATCGAAAAAACTgaagaaa > 2:292587/1‑140 (MQ=255)
gATTTAACAAACGATTCAAATGAAGATGAAATAGAGCAATCATTAAAAGAACCTGCGACTTATAAAGAAGACAGACGTTCATCAGTTGTAATTGATGCA‑AAAAAATT‑ATCGAAAAAACTGAAGAACAATCTTCAGATaaaa < 1:14579/141‑1 (MQ=255)
aCAAACGATTCAAATGAAGATGAAATAGAGCAATCATTAAAAGAACCTGCGACTTATAAAGAAGACAGACGTTCATCAGTTGTAATTGATGCA‑AAAAAATT‑ATCGAAAAAACTGAAGAACAATCTTCAGATAAAAACAaat < 1:293859/141‑1 (MQ=255)
cGATTCAAATGAAGATGAAATAGAGCAATCATTAAAAGAACCTGCGACTTATAAAGAAGACAGACGTTCATCAGTTGTAATTGATGCA‑AAAAAATT‑ATCGAAAAAACTGAAGAACAATCTTCAGATAAAAACAAAtaataa > 2:132782/1‑141 (MQ=255)
cGATTCAAATGAAGATGAAAGATAGCAATCATTAAAAGAACCTGCGACTTATAAAGAAGACAGACGTTCATCAGTTGTAATTGATGCA‑AAAAAATT‑ATCGAAAAAACTGAAGAACAATCTTCAGATAAAAACAAAtaataa < 1:128921/141‑1 (MQ=255)
gAAGATGAAATAGAGCAATCATTAAAAGAACCTGCGACTTATAAAGAAGACAGACGTTCATCAGTTGTAATTGATGCA‑AAAAAATT‑ATCGAAAAAACTGAAGAACAATCTTCAGATAAAAACAAATAATAACAAAGCGCtt < 2:473650/141‑1 (MQ=255)
aTGAAATAGAGCAATCATTAAAAGAACCTGCGACTTATAAAGAAGACAGACGTTCATCAGTTGTAATTGATGCA‑AAAAAATT‑ATCGAAAAAACTGAAGAACAATCTTCAGATAAAAACAAATAATAACAAAGCGCTTGCTa < 2:90314/141‑1 (MQ=255)
tGAAATAGAGCAATCATTAAAAGAACCTGCGACTTATAAAGAAGAAAGACGTTCATCAGTTGTAATTGATGCA‑AAAAAATT‑ATCGAAAAAACTGAAGAACAATCTTCAGATAAAAACAAATAATAACAAAGCGCACGCTAg > 2:332013/1‑141 (MQ=255)
aaaTAGAGCAATCATTAAAAGAACCTGCGACTTATAAAGAAGACAGACGTTCATCAGTTGTAATTGATGCA‑AAAAAATT‑ATCGAAAAAACTGAAGAACAATCTTCAGATAAAAACAAATAATAACAAAGCGCTTGCTAGTa < 1:33633/141‑1 (MQ=255)
aTAGAGCAATCATTAAAAGAACCTGCGACTTATAAAGAAGACAGACGTTCATCAGTTGTAATTGATGCA‑AAAAAATT‑ATCGAAAAAACTGAAGAACAATCTTCAGATAAAAACAAATAATAACAAAGCGCTTGCTAGTAcc > 1:217095/1‑141 (MQ=255)
agagCAATCATTAAAAGAACCTGCGACTTATAAAGAAGACAGACGTTCATCAGTTGTAATTGATGCA‑AAAAAATT‑ATCGAAAAAACTGAAGAACAATCTTCAGATAAAAACAAATAATAACAAAGCGCTTGCTAGTACctc < 1:322172/141‑1 (MQ=255)
gagCAATCATTAAAAGAACCTGCGACTTATAAAGAAGACAGACGTTCATCAGTTGTAATTGATGCA‑AAAAAATT‑ATCGAAAAAACTGAAGAACAATCTTCAGATAAAAACAAATAATAACAAAGCGCTTGCTAGTACctct > 1:462732/1‑141 (MQ=255)
gagCAATCATTAAAAGAACCTGCGACTTATAAAGAAGACAGACGTTCATCAGTTGTAATTGATGCA‑AAAAAATT‑ATCGAAAAAACTGAAGAACAATCTTCAGATAAAAACAAATAATAACAAAGCGCTTGCTAGTACctct < 1:16317/141‑1 (MQ=255)
aTCATTAAAAGAACCTGCGACTTATAAAGAAGACAGACGTTCATCAGTTGTAATTGATGCA‑AAAAAATT‑ATCGAAAAAACTGAAGAACAATCTTCAGATAAAAACAAATAATAACAAAGCGCTTGCTAGTACCTCTTaaaa < 2:51981/141‑1 (MQ=255)
tCATTAAAAGAACCTGCGACTTATAAAGAAGACAGACGTTCAACAGTTGTAATTGATGCA‑AAAAAATT‑ATCGAAAAAACTGAAGAACAATCTTCAGATAAAAACAAATAATAACAAAGCGCTAGCTAGTACCTCTTaaaaa > 2:460113/1‑141 (MQ=255)
aaaGAACCTGCGACTTATAAAGAAGACAGACGTTCATCAGTTGTAATTGATGCA‑AAAAAATT‑ATCGAAAAAACTGAAGAACAATCTTCAGATAAAAACAAATAATAACAAAGCGCTAGCTAGTACCTCTTAAAAAgatgat > 2:112457/1‑141 (MQ=255)
aGAACCTGCGACTTATAAAGAAGACAGACGTTCATCAGTTGTAAATGATGCA‑AAAAAATT‑ATCGAAAAAACTGAAGAACAATCTTCAGATAAAAACAAATAATAACAAAGCGCTTGCTAGTACCTCTTAAAAAGATGATGc < 2:52016/141‑1 (MQ=255)
aCCTGCGACTTATAAANAAGACAGACGTTNATCAGTTGTAATTGATGCA‑AAAAAATT‑ATCGAAAAAACTGAAGAACAATCTTCAGATAAAAACAAATAATAACAAAGCGCTTGCTAGTACCTCTTAAAAAGATGATGCTAg > 1:294082/1‑141 (MQ=255)
aCCTGCGACTTATAAAGAAGACAGACGTTCATCAGTTGTAATTGATGCAAAAAAA‑TT‑ATCGAAAAAACTGAAGAACAATCTTCAGATAAAAACAAATAATAACAAAGCGCTTGCTAGTACCTCTTAAAAAGATGATGCTAg > 1:187774/1‑141 (MQ=255)
gCGACTTATAAAGAAGACAGACGTTCATCAGTTGTAATTGATGCA‑AAAAAATT‑ATCGAAAAAACTGAAGAACAATCTTCAGATAAAAACAAATAATAACAAAGCGCTTGCTAGTACCTCTTAAAAAGATGATGCTAGCAAg > 2:291687/1‑141 (MQ=255)
gCGACTTATAAAGAAGACAGACGTTCATCAGTTGTAATTGATGCA‑AAAAAATT‑ATCGAAAAAACTGAAGAACAATCTTCAGATAAAAACAAATAATAACAAAGCGCTTGCTAGTACCTCTTAAAAAGATGATGCTAGCAAg > 2:26370/1‑141 (MQ=255)
cGACTTATAAAGAAGACAGACGTTCATCAGTTGTAATTGATGCA‑AAAAAATT‑ATCGAAAAAACTgaaga > 2:81727/1‑69 (MQ=255)
cGACTTATAAAGAAGACAGACGTTCATCAGTTGTAATTGATGCA‑AAAAAATT‑ATCGAAAAAACTgaaga < 1:81727/69‑1 (MQ=255)
acatataAAGAAGACAGACGTTCATCAGTTGTAATTGATGCA‑AAAAAATT‑ATCGAAAAAACTGAAGAACAATCTTCAGATAAAAACAAATAATAACAAAGCGCTTGCTAGTACCTCTTAAAAAGATGATGCTAGCAAgcgc < 2:328811/138‑1 (MQ=255)
acagacGTTCATCAGTTGTAATTGATGCA‑AAAAAATT‑ATCGAAAAAACTGAAGAACAATCTTCAGATAAAAACAAATAATAACAAAGCGCTTGCTAGTACCTCTTAAAAAGATGATGCTAGCAAGCGCTTTTctatactat > 1:493820/1‑141 (MQ=255)
caGTTGTAATTGATGCA‑AAAAAATT‑ATCGAAAAAACTGAAGAACAATCTTCAGATAAAAACAAATAATAACAAAGCGCTTGCTAGTACCTCTTAAAAAGATGATGCTAGCAAGCGCTTTTCTATACTATATATTATTTTTc < 2:439987/141‑1 (MQ=255)
aTTGATGCA‑AAAAAATT‑ATCGAAAAAACTGAAGAACAATCTTCAGATAAAAACAAATAATAACAAAGCGCTTGCTAGTACCTCTTAAAAAGATGATGCTAGCAAGCGCTTTTCTATACTATATATTATTTTTCTAAAAttt > 2:156624/1‑141 (MQ=255)
|
AGCAGAATCAGTTAAACAAGCACCACAAAGTGACGATTTAACAAACGATTCAAATGAAGATGAAATAGAGCAATCATTAAAAGAACCTGCGACTTATAAAGAAGACAGACGTTCATCAGTTGTAATTGATGCAGAAAAACAT‑ATCGAAAAAACTGAAGAACAATCTTCAGATAAAAACAAATAATAACAAAGCGCTTGCTAGTACCTCTTAAAAAGATGATGCTAGCAAGCGCTTTTCTATACTATATATTATTTTTCTAAAATTT > CP000730/2455559‑2455824
|
| Alignment Legend |
|---|
Aligned base mismatch/match (shaded by quality score): ATCG/ATCG < 3 ≤ ATCG/ATCG < 12 ≤ ATCG/ATCG < 27 ≤ ATCG/ATCG < 41 ≤ ATCG/ATCG |
Unaligned base: atcg Masked matching base: atcg Alignment gap: ‑ Deleted base: ‑ |
GATK/CNVnator alignment
N/A
