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 |
|
A4 F1 I2 R1
|
780 |
68.3 |
3343050 |
93.5% |
3125751 |
102.9 |
Breseq alignment
BRESEQ :: Evidence
|
| evidence |
seq id |
position |
mutation |
annotation |
gene |
description |
| RA |
NC_000913 |
4,535,441 |
C→T |
pseudogene (439/1029 nt) |
yjhR → |
pseudogene, helicase family, putative frameshift suppressor |
|
| |
seq id |
position |
ref |
new |
freq |
score (cons/poly) |
reads |
annotation |
genes |
product |
| * | NC_000913 | 4,535,441 | 0 | C | T | 98.3%
| 187.9
/ ‑3.7
| 60 | pseudogene (439/1029 nt) | yjhR | pseudogene, helicase family, putative frameshift suppressor |
| Reads supporting (aligned to +/- strand): ref base C (0/0); major base T (28/31); minor base . (1/0); total (29/31) |
| Fisher's exact test for biased strand distribution p-value = 4.83e-01 |
| Kolmogorov-Smirnov test that lower quality scores support variant p-value = 7.79e-01 |
TCTACTCAAAACATGAAGATGGCAGGTTTCTTGATAGCAACAGCACTATCCTCAATGTTGCTGTCTCACGCGCTAAAGATAGTTTTCTGGTATTTGGCGATATGGACCTTATCGAGATGCAGCCCGCATTTTCGCCGCGAGGGTTATTGGCAAAATAT‑CTCTTTTCTTCAGATAATAATGCGTTGCAATTTGAGTTTCAGAAACGACAGGATTTAATTTCCGCACATACACAAATTTCAACGCTGCA > NC_000913/4535319‑4535565
|
tCTACTCAAAACATGAAGATGGCAGGTTTCTTGATAGCAACAGCACTATCCTCAATGTTGCTGTCTCACGCGCTAAAGATAGTTTTCTGGTATTTGGCGATATGGACCTTATCGAGATGCAGTCCGCATTTTCGCcgcg < 2:287679/139‑1 (MQ=255)
tACTCAAAACATGAAGATGGCAGGTTTCTTGATAGCAACAGCACTATCCTCAATGTTGCTGTCTCACGCGCTAAAGATAGTTTTCTGGTATTTGGCGATATGGACCTTATCGAGATGCAGTCCGCATTTTCGCCGCGAg > 2:124297/1‑139 (MQ=255)
aaaaCATGAAGATGGCAGGTTTCTTGATAGCAACAGCACTATCCTCAATGTTGCTGTCTCACGCGCTAAAGATAGTTTTCTGGTATTTGGCGATATGGACCTTATCGAGATGCAGTCCGCATTTTCGCCGCGAGGGTTa < 2:735102/139‑1 (MQ=255)
accATGAAGATGGCAGGTTTCTTGATAGCAACAGCACTATCTTCAATGTTGCTGTCTCACGCGCTAAAGATAGTTTTCTGGTATTTGGTGATATGGACCTTATCGAGATGCAGTCCGCATTTTTGCCGCGAGGGTTAtt > 1:1415054/3‑139 (MQ=255)
aaCATGAAGATGGCAGGTTTCTTGATAGCAACAGCACTATCCTCAATGTTGCTGTCTCACGCGCTAAAGATAGTTTTCTGGTATTTGGCGATATGGACCTTATCGAGATGCAGTCCGCATTTTCGCCGCGAGGGTTAtt > 1:62173/1‑139 (MQ=255)
aCATGAAGATGGCAGGTTTCTTGATAGCAACAGCACTATCCTCAATGTTGCTGTCTCACGCGCTAAAGATAGTTTTCTGGTATTTGGCGATATGGACCTTATCGAGATGCAGTCCGCATTTTCGCCGCGAGGGTTATTg > 1:1567519/1‑139 (MQ=255)
tGAAGATGGCAGGTTTCTTGATAGCAACAGCACTATCCTCAATGTTGCTGTCTCACGCGCTAAAGATAGTTTTCTGGTATTTGGCGATATGGACCTTATCGAGATGCAGTCCGCATTTTCGCCGCGAGGGTTATTGGCa < 2:1415054/139‑1 (MQ=255)
gAAGATGGCAGGTTTCTTGATAGCAACAGCACTATCCTCAATGTTGCTGTCTCACGCGCTAAAGATAGTTTTCTGGTATTTGGCGATATGGACCTTATCGAGATGCAGTCCGCATTTTcgc < 2:1499981/121‑1 (MQ=255)
gAAGATGGCAGGTTTCTTGATAGCAACAGCACTATCCTCAATGTTGCTGTCTCACGCGCTAAAGATAGTTTTCTGGTATTTGGCGATATGGACCTTATCGAGATGCAGTCCGCATTTTcgc > 1:1499981/1‑121 (MQ=255)
cgggTTTCTTGATAGCAACAGCACTATCCTCAATGTTGCTGTCTCACGCGCTAAAGATAGTTTTCTGGTATTTGGCGATATGGACCTTATCGAGATGCAGTCCGCATTTTCGCCGCGAGGGTTATTGGCaa < 2:674906/129‑1 (MQ=255)
cgggTTTCTTGATAGCAACAGCACTATCCTCAATGTTGCTGTCTCACGCGCTAAAGATAGTTTTCTGGTATTTGGCGATATGGACCTTATCGAGATGCAGTCCGCATTTTCGCCGCGAGGGTTATTGGCaa > 1:674906/3‑131 (MQ=255)
cAGGTTTCTTGATAGCAACAGCACTATCCTCAATGTTGCTGTCTCACGCGCTAAAGATAGTTTTCTGGTATTTGGCGATATGGACCTTATCGAGATGCAGTCCGCATTTTCGCCGCGAGGGTTATTGGCAAAATAt‑ctc > 1:943945/1‑139 (MQ=255)
aGGTTTCTTGATAGCAACAGCACTATCCTCAATGTTGCTGTCTCACGCGCTAAAGATAGTTTTCTGGTATTTGGCGATATGGACCTTATCGAGATGCAGTCCGCATTTTCGCCGCGAGGGTTATTGGCAAAATAT‑ctct < 2:227975/139‑1 (MQ=255)
tttCTTGATAGCAACAGCACTATCCTCAATGTTGCTGTCTCACGCGCTAAAGATAGTTTTCTGGTATTTGGCGATATGGACCTTATCGAGATGCAGTCCGCATTTTCGCCGCGAGGGTTATTGGCAAAATAT‑CTCtttt < 2:62173/139‑1 (MQ=255)
aGCAACAGCACTATCCTCAATGTTGCTGTCTCACGCGCTAAAGATAGTTTTCTGGTATTTGGCGATATGGACCTTATCGAGATGCAGTCCGCATTTTCGCCGCGAGGGTTATTGGCAAAatat > 2:406601/1‑123 (MQ=255)
aGCAACAGCACTATCCTCAATGTTGCTGTCTCACGCGCTAAAGATAGTTTTCTGGTATTTGGCGATATGGACCTTATCGAGATGCAGTCCGCATTTTCGCCGCGAGGGTTATTGGCAAAatat < 1:406601/123‑1 (MQ=255)
aGCAACAGCACTATCCTCAATGTTGCTGTCTCACGCGCTAAAGATAGTTTTCTGGTATTTGGCGATATGGACCTTATCGAGATGCAGTCCGCATTTTCGCCGCGAGGGTTATTGGCAAAATAT‑CTCTTTTCTTCAGata > 2:1111412/1‑139 (MQ=255)
gCAACAGCACTATCCTCAATGTTGCTGTCTCACGCGCTAAAGATAGTTTTCTGGTATTTGGCGATATGGACCTTATCGAGATGCAGTCCGCATTTTCGCCGCGAGGGTTATTGGCAAAATAT‑CTCTTTTCTTCAGataa < 2:1567519/139‑1 (MQ=255)
cAGCACTATCCTCAATGTTGCTGTCTCACGCGCTAAAGATAGTTTTCTGGTATTTGGCGATATGGACCTTATCGAGATGCAGTCCGCATTTTCGCCGCGAGGGTTATTGGCaaaa > 2:1343423/1‑115 (MQ=255)
cAGCACTATCCTCAATGTTGCTGTCTCACGCGCTAAAGATAGTTTTCTGGTATTTGGCGATATGGACCTTATCGAGATGCAGTCCGCATTTTCGCCGCGAGGGTTATTGGCaaaa < 1:1343423/115‑1 (MQ=255)
cTCAATGTTGCTGTCTCACGCGCTAAAGATAGTTTTCTGGTATTTGGCGATATGGACCTTATCGAGATGCAGTCCGCATTTTCGCCGCGAGGGTTATTGGCAAAATAT‑CTCTTTTCTTCAGATAATAATGCGTTGCAAt < 1:124297/139‑1 (MQ=255)
aaTGTTGCTGTCTCACGCGCTAAAGATAGTTTTCTGGTATTTGGCGATATGGACCTTATCGAGATGCAGTCCGCATTTTCGCCGCGAGGGTTATTGGCaaaa > 2:1032341/1‑102 (MQ=255)
aaTGTTGCTGTCTCACGCGCTAAAGATAGTTTTCTGGTATTTGGCGATATGGACCTTATCGAGATGCAGTCCGCATTTTCGCCGCGAGGGTTATTGGCaaaa < 1:1032341/102‑1 (MQ=255)
aaTGTTGCTGTCTCACGCGCTAAAGATAGTTTTCTGGTATTTGGCGATATGGACCTTATCGAGATGCAGTCCGCATTTTCGCCGCGAGGGTTATTGGCAAAATAT‑ctct < 2:174518/109‑1 (MQ=255)
aaTGTTGCTGTCTCACGCGCTAAAGATAGTTTTCTGGTATTTGGCGATATGGACCTTATCGAGATGCAGTCCGCATGTTCGCCGCGAGGGTTATTGGCAAAATAT‑ctct > 1:174518/1‑109 (MQ=255)
tGCTGTCTCACGCGCTAAAGATAGTTTTCTGGTATTTGGCGATATGGACCTTATCGAGATGCAGTCCGCATTTTCGCCGCGAGGGTTATTGGCAAAATAT‑CTCTTttcttc < 1:1550152/111‑1 (MQ=255)
tGCTGTCTCACGCGCTAAAGATAGTTTTCTGGTATTTGGCGATATGGACCTTATCGAGATGCAGTCCGCATTTTCGCCGCGAGGGTTATTGGCAAAATAT‑CTCTTttcttc > 2:1550152/1‑111 (MQ=255)
tcACGCGCTAAAGATAGTTTTCTGGTATTTGGCGATATGGACCTTATCGAGATGCAG‑TCGCAATTTTGCCGGCGGGGGTATTTGCCAAATATCCTCTTTT‑TTCAGGTTATTATTGGTTTCAATTTGaactgttcccttt > 2:1536358/1‑127 (MQ=255)
cgcgCTAAAGATAGTTTTCTGGTATTTGGCGATATGGACCTTATCGAGATGCAGTCCGCATTTTCGCCGCGAGGGTTATTGGCAAAatat < 1:1501631/90‑1 (MQ=255)
cgcgCTAAAGATAGTTTTCTGGTATTTGGCGATATGGACCTTATCGAGATGCAGTCCGCATTTTCGCCGCGAGGGTTATTGGCAAAatat > 2:1501631/1‑90 (MQ=255)
cgcgCTAAAGATAGTTTTCTGGTATTTGGCGATATGGACCTTATCGAGATGCAGTCCGCATTTTCGCCGCGAGGGTTATTGGCAAAATAT‑CTCTTTTCTTCAGATAATAATGCGTTGCAATTTGAGTTTCAGAAACGAc > 1:743517/1‑139 (MQ=255)
cgcgCTAAAGATAGTTTTCTGGTATTTGGCGATATGGACCTTATCGAGATGCAGTCCGCATTTTCGCCGCGAGGGTTATTGGCAAAATAT‑CTCTTTTCTTCAGATAATAATGCGTTGCAATTTGAGTTTCAGAAACGAc < 2:943945/139‑1 (MQ=255)
aaGATAGTTTTCTGGTATTTGGCGATATGGACCTTATCGAGATGCAGTCCGCATTTTCGCCGCGAGGGTTATTgg > 1:1486772/1‑75 (MQ=255)
aaGATAGTTTTCTGGTATTTGGCGATATGGACCTTATCGAGATGCAGTCCGCATTTTCGCCGCGAGGGTTATTgg < 2:1486772/75‑1 (MQ=255)
tttCTGGTATTTGGCGATATGGACCTTATCGAGATGCAGTCCGCATTTTCGCCGCGAGGGTTATTGGCAAAATAT‑CTCTTTTCTTCAGATAATAATGCGTTGCAATTTGAGTTTCAGAAACGACAGGATTTAATTTCCg < 1:1111412/139‑1 (MQ=255)
tCTGGTATTTGGCGATATGGACCTTATCGAGATGCAGTCCGCATTTTcgcc > 1:1662071/1‑51 (MQ=255)
tCTGGTATTTGGCGATATGGACCTTATCGAGATGCAGTCCGCATTTTcgcc < 2:1662071/51‑1 (MQ=255)
ttGGCGATATGGACCTTATCGAGATGCAGTCCGCATTTTCGCCGCGAGGGTTATTGGCAAAATAT‑CTCTTTTCTTCAGATAATAATGCGTTGCAATTTGAGTTTCAGAAACGACAGGATTTAATTTCCGCACATAcaca < 2:657347/139‑1 (MQ=255)
tGGCGATATGGACCTTATCGAGATGCAGTCCGCATTTTCGCCGCGAGGGTTATTGGCAAAATAT‑CTCTTTTCTTCAGATAATAATGCGTTGCAATTTGAGTTTCAGAAACGACAGGATTTAATTTCCGCACATACACaa > 1:905378/1‑139 (MQ=255)
ggCGATATGGACCTTATCGAGATGCAGTCCGCATTTTCGCCGCGAGGGTTATTGGCAAAATAT‑CTCTTTTCTTCAGATAATAATGCGTTGCAATTTGAGTTTCAGAAACGAc < 1:24950/112‑1 (MQ=255)
ggCGATATGGACCTTATCGAGATGCAGTCCGCATTTTCGCCGCGAGGGTTATTGGCAAAATAT‑CTCTTTTCTTCAGATAATAATGCGTTGCAATTTGAGTTTCAGAAACGAc > 2:24950/1‑112 (MQ=255)
gATATGGACCTTATCGAGATGCAGTCCGCATTTTCGCCGCGAGGGTTATTGGCAAAATAT‑CTCTTTTCTTCAGATAATAATGCGTTGCAATTTGAGTTTCAGAAACGACAGGATTTAATTTCCGCACATACACAAAttt < 2:905378/139‑1 (MQ=255)
tatGGACCTTATCGAGATGCAGTCCGCATTTTCGCCGCGAGGGTTATTGGCAAAATAT‑CTCTTTTCTTCAGATAATAATGCGTTGCAATTTGAGTTTCAGAAACGACAGGATTTAATTTCCGCACATACACAAATTTCa > 1:582760/1‑139 (MQ=255)
ttATCGAGATGCAGTCCGCATTTTCGCCGCGAGGGTTATTGGCAAAATAT‑CTCTTTTCTTCAGATAATAATGCGTTGCAATTTGAGTTTCAGAAACGACAGGATTTAATTTCCGCACATACACAAATTTCAACGCTGCa < 2:582760/139‑1 (MQ=255)
tATCGAGATGCAGTCCACATTTTCGCCGCGAGGGTTa > 1:1218575/1‑37 (MQ=255)
tATCGAGATGCAGTCCACATTTTCGCCGCGAGGGTTa < 2:1218575/37‑1 (MQ=255)
aTCGAGATGCAGTCCGCATTTTCGCCGCGAGGGTTATTGGCAAAATAT‑CTCTTTTCTTCAGATAATAATGCGTTGCAATTTGAGtt < 1:1490780/86‑1 (MQ=255)
aTCGAGATGCAGTCCGCATTTTCGCCGCGAGGGTTATTGGCAAAATAT‑CTCTTTTCTTCAGATAATAATGCGTTGCAATTTGAGtt > 2:1490780/1‑86 (MQ=255)
aTCGAGATGCAGTCCGCATTTTCGCCGCGAGGGTTATTGGCAAAATAT‑CTCTTTTCTTCAGATAATAATGCGTTGCAATTTGAGTTTCAGAAACGACAg < 1:905111/99‑1 (MQ=255)
aTCGAGATGCAGTCCGCATTTTCGCCGCGAGGGTTATTGGCAAAATAT‑CTCTTTTCTTCAGATAATAATGCGTTGCAATTTGAGTTTCAGAAACGACAg > 2:905111/1‑99 (MQ=255)
aTCGAGATGCAGTCCGCATTTTCGCCGCGAGGGTTATTGGCAAAATAT‑CTCTTTTCTTCAGATAATAATGCGTTGCAATTTGAGTTTCAGAAACGACAGGATTTAATTTCCGCACAt > 1:834855/1‑117 (MQ=255)
aTCGAGATGCAGTCCGCATTTTCGCCGCGAGGGTTATTGGCAAAATAT‑CTCTTTTCTTCAGATAATAATGCGTTGCAATTTGAGTTTCAGAAACGACAGGATTTAATTTCCGCACAt < 2:834855/117‑1 (MQ=255)
aTCGAGATGCAGTCCGCATTTTCGCCGCGAGGGTTATTGGCAAAATAT‑CTCTTTTCTTCAGATAATAATGCGTTGCAATTTGAGTTTCAGAAACGACAGGATTTAATTTCCGCACATACACAAATTTCAACGCTGCa < 1:1279966/137‑1 (MQ=255)
aTCGAGATGCAGTCCGCATTTTCGCCGCGAGGGTTATTGGCAAAATAT‑CTCTTTTCTTCAGATAATAATGCGTTGCAATTTGAGTTTCAGAAACGACAGGATTTAATTTCCGCACATACACAAATTTCAACGCTGCa > 2:1279966/1‑137 (MQ=255)
aTGCAGTCCGCATTTTCGCCGCGAGGGTTATTGGCAAAATAT‑CTCTTttcttc < 1:1338497/53‑1 (MQ=255)
aTGCAGTCCGCATTTTCGCCGCGAGGGTTATTGGCAAAATAT‑CTCTTttcttc > 2:1338497/1‑53 (MQ=255)
tGCAGTCCGCATTTTCGCCGCGAGGGTTATTGGCAAAATAT‑CTCTTTTCTTCAGATAATAATGCGTTGCAATTTGAGTTTCAGAAACGAc > 1:465836/1‑90 (MQ=255)
tGCAGTCCGCATTTTCGCCGCGAGGGTTATTGGCAAAATAT‑CTCTTTTCTTCAGATAATAATGCGTTGCAATTTGAGTTTCAGAAACGAc < 2:465836/90‑1 (MQ=255)
tGCAGTCCGCATTTTCGCCGCGAGGGTTATTGGCAAAATAT‑CTCTTTTCTTCAGATAATAATGCGTTGCAATTTGAGTTTCAGAAACGACAGGATTTAATTTCCGCACATACACAAATTTCAACGCTGCa > 1:557584/1‑130 (MQ=255)
tGCAGTCCGCATTTTCGCCGCGAGGGTTATTGGCAAAATAT‑CTCTTTTCTTCAGATAATAATGCGTTGCAATTTGAGTTTCAGAAACGACAGGATTTAATTTCCGCACATACACAAATTTCAACGCTGCa < 2:557584/130‑1 (MQ=255)
|
TCTACTCAAAACATGAAGATGGCAGGTTTCTTGATAGCAACAGCACTATCCTCAATGTTGCTGTCTCACGCGCTAAAGATAGTTTTCTGGTATTTGGCGATATGGACCTTATCGAGATGCAGCCCGCATTTTCGCCGCGAGGGTTATTGGCAAAATAT‑CTCTTTTCTTCAGATAATAATGCGTTGCAATTTGAGTTTCAGAAACGACAGGATTTAATTTCCGCACATACACAAATTTCAACGCTGCA > NC_000913/4535319‑4535565
|
| Alignment Legend |
|---|
Aligned base mismatch/match (shaded by quality score): ATCG/ATCG < 3 ≤ ATCG/ATCG < 16 ≤ ATCG/ATCG < 34 ≤ ATCG/ATCG < 39 ≤ ATCG/ATCG < 40 ≤ ATCG/ATCG |
Unaligned base: atcg Masked matching base: atcg Alignment gap: ‑ Deleted base: ‑ |
GATK/CNVnator alignment
N/A
