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 |
|
A21 F117 I0 R1
|
36 |
24.6 |
540534 |
94.7% |
511885 |
140.9 |
Breseq alignment
BRESEQ :: Evidence
|
| evidence |
seq id |
position |
mutation |
freq |
annotation |
gene |
description |
| RA |
CP000730 |
2,455,698 |
2 bp→AT |
100% |
coding (1216‑1217/1260 nt) |
USA300HOU_2315 → |
hypothetical membrane protein |
|
| |
seq id |
position |
ref |
new |
freq |
score (cons/poly) |
reads |
annotation |
genes |
product |
| * | CP000730 | 2,455,698 | 0 | C | A | 93.9%
| 85.8
/ 0.8
| 33 | coding (1216/1260 nt) | USA300HOU_2315 | hypothetical membrane protein |
| Reads supporting (aligned to +/- strand): ref base C (0/1); major base A (19/11); minor base . (1/1); total (20/13) |
| Fisher's exact test for biased strand distribution p-value = 1.00e+00 |
| Kolmogorov-Smirnov test that lower quality scores support variant p-value = 9.01e-01 |
| Rejected as polymorphism: E-value score below prediction cutoff. |
| 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. |
| * | CP000730 | 2,455,699 | 0 | A | T | 100.0%
| 81.0
/ ‑6.5
| 36 | H406L (CAT→CTT) | USA300HOU_2315 | hypothetical membrane protein |
| Reads supporting (aligned to +/- strand): ref base A (0/1); major base T (20/14); minor base C (0/1); total (20/16) |
| 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. |
CAGTTAAACAAGCACCACAAAGTGACGATTTAACAAACGATTCAAATGAAGATGAAATAGAGCAATCATTAAAAGAACCTGCGACTTATAAAGAAGACAGACGTTCATCAGTTGTAATTGATGCAGAAAAACATATCGAAAAAACTGAAGAACAATCTTCAGATAAAAACAAATAATAACAAAGCGCTTGCTAGTACCTCTTAAAAAGATGATGCTAGCAAGCGCTTTTCTATACTATATATTATTTTTCTAAAATTTTAACACCCT > CP000730/2455567‑2455833
||
cAGTTAAACAAGCACCACAAAGTGACGATTTAACAAACGATTCAAATGAAGATGAAATAGAGCAATCATTAAAAGAACCTGCGACTTATAAAGAAGACAGACGTTCATCAGTTGTAATTGATGCA‑AAAAAATTATCGaaaa > 1:143484/1‑141 (MQ=255)
caccacAAAGTGACGATTTAACAAACGATTCAAATGAAGATGAAATAGAGCAATCATTAAAAGAACCTGCGACTTATAAAGAAGACAGACGTTCATCAGTTGTAATTGATGCA‑AAAAAATTATCGAAGAAACTGAAGAACa > 2:195011/1‑141 (MQ=255)
ccacAAAGTGACGATTTAACAAACGATTCAAATGAAGATGAAATAGAGCAATCATTAAAAGAACCTGCGACTTATAAAGAAGACAGACGTTCATCAGTTGTAATTGATGCA‑AAAAAATTATCGAAAAAACTGAAGAACAAt > 1:253223/1‑141 (MQ=255)
ccacAAAGTGACGATCTAACAAACGATTCAAATGAAGATGAAATAGAGCAATCATTAAAAGAACCTGCGACTTATAAAGAAGACAGACGTTCATCAGTTGTAATTGATGCA‑AAACACCTATCGAAAGATCTGAAGAACAAt < 2:260336/141‑1 (MQ=255)
acaAAGTGACGATTTAACAAACGATTCAAAGAAAGATGAAATAGAGCAATCATTAAAAGAACCTGCGACTTATAAAGAAGACCGTCGTGCAGCAGTTGT‑ATTGCGGTCAAAAAAATTATCGAAAAAACTGAAGAACAATCt < 1:130058/141‑1 (MQ=255)
aaaGTGACGATTTAACAAACGATTCAAATGAAGATGAAATAGAGCAATCATTAAAAGAACCTGCGACTTATAAAGAAGACAGACGTTCATCAGTTGTAATTGATGCAAAAAAA‑TTATCGAAAAAACTGAAGAACAATCtta > 2:182865/1‑140 (MQ=255)
aaaGTGACGATTTAACAAACGATTCAAATGAAGATGAAATAGAGCAATCATTAAAAGAACCTGCGACTTATAAAGAAGACAGACGTTCATCAGTTGTAATTGATGCA‑AAAAAATTATCGAAAAACCTGAAGAACAATCTTc > 2:263564/1‑141 (MQ=255)
aaaGTGACGATTTAACAAACGATTCAAATGAAGATGAAATAGAGCAATCATTAAAAGAACCGGGCACTTATAGAGAAGACAGACGTTCATCAGTTGTAATTGATGCA‑AAAAAATTATCGAAAAAAATGAAGAACAATATTc > 2:230994/1‑141 (MQ=255)
aCGATTTAACAAACGATTCAAATGAAGATGAAATAGAGCAATCATTAAAAGAACCTGCGACTTATAAAGAAGACAGACGTTCATCAGTTGTAATTGATGCA‑AAAAAATTATCGAAAAAACTGAAGAACAATCTTCAGATaa > 1:255977/1‑141 (MQ=255)
aCGATTTAACAAACGATTCAAATGAAGATGAAATAGAGCAATCAATAAAAGAACCTGCGACTTATAAAGAAGACAGACGTTCATCAGTTGTAATTGATGCA‑AAAAAATTATCGAAAAAACTGAAGAACAATCTTCAGATaa > 2:144305/1‑141 (MQ=255)
ttCAAATGAAGATGAAATAGAGCAATCATTAAAAGAACCTGCGACTTATAAAGAAGACAGACGTTCATCAGTTGTAATTGATGCA‑AAAAAATTATCGAAAAAACTGAAGAACAATCTTCAGATAAAAACAAATAATAACaa > 2:141139/1‑141 (MQ=255)
ttCAAATGAAGATGAAAGAGAGCAATCATTAAAAGAACCTGCGACTTATAAAGAAGACAGACGTTCATCAGTTGTAATGGATGCAAAAAAA‑TTATCGAAAAAACTGAAGAACAATCTTCAGATAAAAACAAATAATAACaa < 1:171563/141‑1 (MQ=255)
tCACATGAAGAACAAAAAGAGCAATCTTGAAGAGAACCCGCGACTTATAAAGAAGACAGACGTTCATAAGTTGTAATTGATGCA‑AAACAATTATCGAAAAAACTGAAGAACAATCTTCAGAAAAAAacaaacaaacacgaa > 2:269560/1‑134 (MQ=255)
gttagaaTAGAGCAATCATTAAAAGAACCTTCGACTTATAAAGAAGACAGACGTTCATCAGTTGTAATTGATGCA‑AAAAAATTATCGAAAAAACTGAAGAACAATCATCAGATAAAAACAAATAATAACAAAGCGCTTGCt < 1:123199/136‑1 (MQ=255)
gATGAAATGGAGCAATCATTAAAAGATCCGTCGACTTAGAAAGAAGACAGACAGTCATAAGTTGCAATGTATTCA‑AAAAAATTATCGAAAAAGCTGAAGAACAATCTTCAGATAAAAACAATTAAGAACAAAGCGCTGGCt < 2:29078/141‑1 (MQ=255)
aaaTAGAGCAATCATTAAAAGAACCTGCGACTTATAAAGAAGACAGACGTTCATCAGTTGTAATTGATGCA‑AAAAAATTATCGAAAAAACTGAAGAACAATCTTCAGATAAAAACAAATAATAACAAAGCGCTTGCTAGTa < 1:268117/141‑1 (MQ=255)
aTAGAGCAATCATTAAAAGAACCTGCGACTTATAAAGAAGACAGACGTTCATCAGTTGTAATTGATGCA‑AAAAAATTATCGAAAAAACTGAAGAACAATCTTCAGATAAAAACAAATAATAACAAAGCGCTTGCTAGTAcc > 2:78287/1‑141 (MQ=255)
agCAATCATTAAAAGAACCTGCGACTTATAAAGAAGACAGACGTTCATCAGTTGTAATTGATGCA‑AAAAAATTATCGAAAAAACTGAAGAACAATCTTCAGATAAAAACAAATAATAACAAAGCGCTTGCTAGTACCTCtt > 1:268823/1‑141 (MQ=255)
agCAATCATCAAAAGAACCTGCGAATTATAAAGAAGACAGACGTTCATCAATTGTTGTTGTTGCA‑AAAATATTATCGAAAAAACTGAAGAACAATCTTCAGATAAAAACAAATAATAACAAAGCGCTAGCTAGTACCTCtt > 1:197813/1‑141 (MQ=255)
gCAATCATTAAAAGAACCTGCGACTTATAAAGAAGACAGACGTTCATCAGTTGTAATTGATGCA‑AAAAAATTATCGAAAAAACTGAAGAACAATCTTCAGATAAAAACAAATAATAACAAAGCGCTTGCTAGTACCTCTTa > 2:136065/1‑141 (MQ=255)
cAATCATTACAAGAACCTGCGCCTTATAAAGAAGACAGACGTGCATCAATATTAATTGATGCA‑AAGAAATTATCGAAAAAACTGAAGAACAATCTTCAGATAAAAACAAATACAAACAAACCGCATACTAGTaattctaca > 2:84564/1‑133 (MQ=255)
taTTAAAATAACCTTCGAATTATAAAGAAGACAGACGTTCATTATTTGTAATTGATGCA‑AAAAAATTATCGAAAAAACTGAAGAACAATCTTCAGATAAAAACAAATAATAACAAAGCGCTTGCTAGTACCTCTTAAAAAg < 1:63781/140‑1 (MQ=255)
cggCGACTTATAAAGAAGACAGACGTTCATCAGTTGCAATTGATGCA‑AAAAAATTATCGAAAAAACTGAAGAACAATCTTCAGATAAAAACAAATAATAACAAAGCGCTTGCTAGTACCTCTTAAAAAGATGATGCTAGCa < 2:73539/139‑1 (MQ=255)
cTGCGACTTATAAAGAAGACAGACGTTCATCAGTTGTAATTGATGCA‑AAAAAATTATCGAAAAAACTGAAGAACAATCTTCAGATAAAAACAAATAATAACAAAGCGCTTGCTAGTACCTCTTAAAAAGATGATGCTAGCa < 1:4402/141‑1 (MQ=255)
tGCGACTTATAAAGAAGACAGACGTTCATCAGTTGTAATTGATGCA‑AAAAAATTATCGAAAAAACTGAAGAACAATCTTCAGATAAAAACAAATAATAACAAAGCGCTTGCTAGTACCTCTTAAAAAGATGATGCTAGCaa < 1:14418/141‑1 (MQ=255)
tGCGACTTATAAAGAAGACAGACGTTCATCAGTTGTAATTGATGCA‑AAAAAATTATCGAAAAAACTGAAGAACAATCTTCAGATAAAAACAAATAATAACAAAGCGCTGGCTAGTACCTCTTAAAAAGATGAGGCTAGCaa > 1:41374/1‑141 (MQ=255)
acgaagaCAGACGTTCATCAGTTGTAATTGATGCA‑AAAAAATTATCGAAAAAACTGAAGAACAATCTTCAGATAAAAACAAATAATAACAAAGCGCTTGCTAGTACCTCTTAAAAAGATGATGCTAGCAAGCGCTTTTcta < 1:15212/139‑1 (MQ=255)
aagtagACAGACGTTCATCAGTTGTAATTGATGCA‑AAAAAATTATCGAACAAACTGAAGAACAATCTTCAGATAAAAACAAATAATAACAAAGCGCTTGCTCGTACCTCTTAAAAAAATGATGCTAACAAGAGCTTTTcta > 2:3860/1‑141 (MQ=255)
acagacGTGCATCAGTTGTAATTGATGCA‑AAAAAAATATCGAAAAAACTGAAGAACAATCTTCAGATAAAAACAAATAATAACAAAGCGCTTGCTAGTACCTCTTAAAAAGATGATGCTAGCAAGCGCTTTTctatactat < 2:179832/141‑1 (MQ=255)
agacGTTCATCAGTTGTAATTGATGCA‑AAAAAATTATCGAAAAAACTGAAGAACAATCTTCAGATAAAAACAAATAATAACAAAGCGCTTGCTAGTACCTCTTAAAAAGATAATGCTAGCAAGCGCTTTTCTATACtatat > 1:65749/1‑141 (MQ=255)
acGTTCAGCAGTTGTAATTGATG‑AAAAAAAATTATCGAAAAAACTGAAGAACAATCTTCAGATAAAAACAAATAATTACAAAGCGCTTGCTAGTACCTCTTAAAAAGATGATGCTAGCAAGCGCTTTTCTATACTatatat < 2:188447/141‑1 (MQ=255)
tcaGTTGTAATTGATGCA‑AAAAAATTATCGAAAAAACTGAAGAACAATCTTCAGATAAAAACAAATAATAACAAAGCGCTTGCTAGTACCTCTTAAAAAGATGATGCTAGCAAGCGCTTTTCTATACTATATATTAttttt > 2:32961/1‑141 (MQ=255)
aTTGATGCA‑AAAAAATTATCGAAAAAACTGAAGAACAATCTTCAGATAAAAACAAATAATAACAAAGCGCTTGCTAGTACCTCTTAAAAAGATGATGCTAGCAAGCGCTTTTCTATACTATATATTATTTTTCTAAAAttt > 1:110195/1‑141 (MQ=255)
ttgaagaaaaaaaaTTATCGAAAAAACCGAAGAACAATCTTCAGATAAAAACCAATAATAACAAAGCGCTTGCTAGTAACTCTTAAAAAGATGATTCTAGCAATCGCTTTTCTATACTATATATTATTTTTCTAAAAtttt < 1:93371/133‑1 (MQ=255)
caaaaaaaTTATCGAAAAAACTGAAGAACAATCTTCAGATAAAAACAAATAATAACAAAGCGCTTGCTAGTACCTCTTAAAAAGATGATGCTAGCAAGCGCTTTTCTATACTATATATTATTTTTCTAAAATTTTAACAcc < 1:70636/139‑1 (MQ=255)
aaaaaaTTATCGAAAAAACTGAAGAACAATCTTCAGATAAAAACAAATAATAACAAAGCGCTTGCTAGTACCTCTTAAAAAGATGATGCTAGCAAGCGCTTTTCTATACTATATATTATTTTTCTAAAATTTTAACACCct < 1:205832/141‑1 (MQ=255)
||
CAGTTAAACAAGCACCACAAAGTGACGATTTAACAAACGATTCAAATGAAGATGAAATAGAGCAATCATTAAAAGAACCTGCGACTTATAAAGAAGACAGACGTTCATCAGTTGTAATTGATGCAGAAAAACATATCGAAAAAACTGAAGAACAATCTTCAGATAAAAACAAATAATAACAAAGCGCTTGCTAGTACCTCTTAAAAAGATGATGCTAGCAAGCGCTTTTCTATACTATATATTATTTTTCTAAAATTTTAACACCCT > CP000730/2455567‑2455833
|
| Alignment Legend |
|---|
Aligned base mismatch/match (shaded by quality score): ATCG/ATCG < 3 ≤ ATCG/ATCG < 12 ≤ ATCG/ATCG < 13 ≤ ATCG/ATCG < 32 ≤ ATCG/ATCG < 41 ≤ ATCG/ATCG |
Unaligned base: atcg Masked matching base: atcg Alignment gap: ‑ Deleted base: ‑ |
GATK/CNVnator alignment
N/A
