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 |
|
A11 F1 I1 R1
|
757 |
76.1 |
3598070 |
93.4% |
3360597 |
108.6 |
Breseq alignment
BRESEQ :: Evidence
|
| evidence |
seq id |
position |
mutation |
annotation |
gene |
description |
| RA |
NC_000913 |
3,815,863 |
C→T |
pseudogene (19/48 nt) |
rph ← |
ribonuclease PH (defective),enzyme, Degradation of RNA, RNase PH |
|
| |
seq id |
position |
ref |
new |
freq |
score (cons/poly) |
reads |
annotation |
genes |
product |
| * | NC_000913 | 3,815,863 | 0 | C | T | 97.8%
| 137.5
/ NA
| 45 | pseudogene (19/48 nt) | rph | ribonuclease PH (defective),enzyme, Degradation of RNA, RNase PH |
| Reads supporting (aligned to +/- strand): ref base C (0/0); major base T (22/22); minor base G (1/0); total (23/22) |
| Fisher's exact test for biased strand distribution p-value = 1.00e+00 |
| Kolmogorov-Smirnov test that lower quality scores support variant p-value = 1.00e+00 |
GGCGCTGATATGGTTTCATGCCTTCGCTCCTCATCTTACTTTTCTACAGACAAAAAAA‑AGGCGACTCATCAGTCGCCTTAAAAATCAGTTTGCCAGCGCCGCCTTCTGCGTCGCTACAATGGATTCGATTCCCCTCGGGCCAGAGCCAACAAGATGAGTAGCTCTTCATGGGTGAACGGCTCGCCTTCTGCCGTCCCCTGCACTTCAATGATGCGCCCGTCTTCGG > NC_000913/3815750‑3815975
|
ggCGCTGATATGGTTTCATGCCTTCGCTCCTCATCTTACTTTTCTACAGACAAAAAAA‑AGGCGACTCATCAGTCGCCTTAAAAATCAGTTTGCCGGCGCCGCCTTCTGCGTCGTTACAATGGATTCGATTCCCCTCggg < 2:875257/139‑1 (MQ=255)
atGGTTTCATGCCTTCGCTCCTCATCTTACTTTTCTACAGACAAAAAAA‑AGGCGACTCATCAGTCGCCTTAAAAATCAGTTTGCCGGCGCCGCCTTCTGCGTCGTTACAATGGATTCGATTCCCCTCGGGCCAGAGCca < 1:26503/139‑1 (MQ=255)
atGGTTTCATGCCTTCGCCCCTCATCTTACTTTTCTACAGACAAAAAAA‑AGGCGACTCATCAGTCGCCTTAAAAATCAGTTTGCCGGCGCCGCCTTCTGCGTCGTTACAATGGATTCGATTCCCCTCGGGCCAGAGCca < 2:1207939/139‑1 (MQ=255)
aTGCCTTCGCTCCTCATCTTACTTTTCTACAGACAAAAAAA‑AGGCGACTCATCAGTCGCCTTAAAAATCAGTTTGCCGGCGCCGCCTTCTGCGTCGTTACAAt > 2:836322/1‑103 (MQ=255)
aTGCCTTCGCTCCTCATCTTACTTTTCTACAGACAAAAAAA‑AGGCGACTCATCAGTCGCCTTAAAAATCAGTTTGCCGGCGCCGCCTTCTGCGTCGTTACAAt < 1:836322/103‑1 (MQ=255)
gCCTTCGCTCCTCATCTTACTTTTCTACAGACAAAAAAA‑AGGCGACTCACCAGTCGCCTTAAAAATCAGTTTGCCGGCGCCGCCTTCTGCGTCGTTACAATGGATTCGATGCCCCTCGGGCAAGAGCCAACAAGATGAg < 1:1057397/139‑1 (MQ=255)
aCTTTTCTACAGACAAAAAAA‑AGGCGACTCATCAGTCGCCTTAAAAATCAGTTTGCCGGCGCCGCCTTCTGCGTCGTTACAATGGATTCGATTCCCCTCGGGCCAGAGCCAACAAGATGAGTAGCTCTTCATGGGTGaa > 2:1417654/1‑139 (MQ=255)
ttttCTACAGACAAAAAAATAGGCGCCTCATCGGTCGCCTTAAAATTCAGTTTGCCGGCGCCGCCTTTTGCGTCGTTACAATGATTTCGATTCCCCTCGGGCCAGGCCCAACAAGATGAGTAGCTCTTCATGGGTGAAc > 2:1197715/1‑139 (MQ=255)
ttttCTACAGACAAAAAAA‑AGGCGACTCATCAGTCGCCTTAAAAATCAGTTTGCCGGCGCCGCCTTCTGCGTCGTTACAATGGATTCGATTCCCCTCGGGc < 1:1363885/101‑1 (MQ=255)
ttttCTACAGACAAAAAAA‑AGGCGACTCATCAGTCGCCTTAAAAATCAGTTTGCCGGCGCCGCCTTCTGCGTCGTTACAATGGATTCGATTCCCCTCGGGc > 2:1363885/1‑101 (MQ=255)
tACAGACAAAAAAA‑AGGCGACTCATCAGTCGCCTTAAAAATCAGTTTGCCGGCGCCGCCTTCTGCGTCGTTACAATGGATTCGATTCCCCTCGGGCCAGAGCCAACAAGATGAGTAGCTCTTCATGGGTGAACGGCTCg > 2:1352970/1‑139 (MQ=255)
cAGACAAAAAAA‑AGGCGACTCATCAGTCGCCTTAAAAATCAGTTTGCCGGCGCCGCCTTCTGCGTCGTTACAATGGATTCGATTCCCCTCGGGc < 2:310864/94‑1 (MQ=255)
cAGACAAAAAAA‑AGGCGACTCATCAGTCGCCTTAAAAATCAGTTTGCCGGCGCCGCCTTCTGCGTCGTTACAATGGATTCGATTCCCCTCGGGc > 1:310864/1‑94 (MQ=255)
aaaaaaa‑aGGCGACTCATCAGTCGCCTTAAAAATCAGTTTGCCGGCGCCGCCTTCTGCGTCGTTACAATGGATTCGATTCCCCTCGGGCCAGAGCCAACAAGATGAGTAg > 1:1231125/1‑110 (MQ=255)
aaaaaaa‑aGGCGACTCATCAGTCGCCTTAAAAATCAGTTTGCCGGCGCCGCCTTCTGCGTCGTTACAATGGATTCGATTCCCCTCGGGCCAGAGCCAACAAGATGAGTAg < 2:1231125/110‑1 (MQ=255)
aaaaaaa‑aGGCGACTCATCAGTCGCCTTAAAAATCAGTTTGCCGGCGCCGCCTTCTGCGTCGTTACAATGGATTCGATTCCCCTCGGGCCAGAGCCAACAAGATGAGTAGCTCTTCATGGGTGAACGGCTCGCCTTCTg > 2:1364527/1‑139 (MQ=255)
aa‑aGGCGACTCATCAGTCGCCTTAAAAATCAGTTTGCCGGCGCCGCCTTCTGCGTCGTTACAATGGATTCGATTCCCCTCGGGCCAGAGCCAACAAGATGAGTAGCTCTTCATGGGTGAACGGCTCGCCTTCTGCCGTc < 1:1352970/139‑1 (MQ=255)
ggCGACTCATCAGTCGCCTTAAAAATCAGTTTGCCGGCGCCGCCTTCTGCGTCGTTACAATGGATTCGATTCCCCTCGGGCCAGAGCcaac > 2:176806/1‑91 (MQ=255)
ggCGACTCATCAGTCGCCTTAAAAATCAGTTTGCCGGCGCCGCCTTCTGCGTCGTTACAATGGATTCGATTCCCCTCGGGCCAGAGCcaac < 1:176806/91‑1 (MQ=255)
ggCGACTCATCAGTCGCCTTAAAAATCAGTTTGCCGGCGCCGCCTTCTGCGTCGTTACAATGGATTCGATTCCCCTCGGGCCAGAGCCAACAAGATGAGTAGCTCTTCATGGGTGAACGGCTCGCCTTCTGCCGTcccc < 2:1729/139‑1 (MQ=255)
ggCGACTCATCAGTCGCCTTAAAAATCAGTTTGCCGGCGCCGCCTTCTGCGTCGTTACAATGGATTCGATTCCCCTCGGGCCAGAGCCAACAAGATGAGTAGCTCTTCATGGGTGAACGGCTCGCCTTCTGCCGTcccc > 2:145362/1‑139 (MQ=255)
cGACTCATCAGTCGCCTTAAAAATCAGTTTGCCGGCGCCGCCTTCTGCGTCGTTACAATGGATTCGATTCCCCt < 1:697776/74‑1 (MQ=255)
cGACTCATCAGTCGCCTTAAAAATCAGTTTGCCGGCGCCGCCTTCTGCGTCGTTACAATGGATTCGATTCCCCt > 2:697776/1‑74 (MQ=255)
cGACTCATCAGTCGCCTTAAAAATCAGTTTGCCGGCGCCGCCTTCTGCGTCGTTACAATGGATTCGATTCCCCTCGGGCCAGAGCCAACAAGATGAGTAGCTCTTCATGGGTGAACGGCTCGCCTTCTGCCGTCCCCTg < 1:411206/139‑1 (MQ=255)
atcaGTCGCCTTAAAAATCAGTTTGCCGGCGCCGCCTTCTGCGTCGTTACAATGGATTCGATTCCCCTCGGGCCAGAGCCAACAAGATGAGTAGCTCTTCATGGGTGAACGGCTCGCCTTCTGCCGTCCCCTGCACTTc > 1:859344/1‑139 (MQ=255)
aGTCGCCTTAAAAATCAGTTTGCCGGCGCCGCCTTCTGCGTCGTTACAATGGATTCGATTCCCCt > 2:416962/1‑65 (MQ=255)
aGTCGCCTTAAAAATCAGTTTGCCGGCGCCGCCTTCTGCGTCGTTACAATGGATTCGATTCCCCt < 1:416962/65‑1 (MQ=255)
gTCGCCTTAAAAATCAGTTTGCCGGCGCCGCCTTCTGCGTCGTTACAATGGATTCGATTCCCCTCGGGCCAGAGCCAACAAGATGAGTAGCTCTTCATGGGTGAACGGCTCGCCTTCTGCCGTCCCCTGCACTTCAatg > 2:1394652/1‑139 (MQ=255)
gCCTTAAAAATCAGTTTGCCGGCGCCGCCTTCTGCGTCGTTACAATGGATTCGATTCCCCTCGGGCCAGAGCCAACAAGATGAGTAGCTCTTCATGGGTGAACGGCTCGCCTTCTGCCGTCCCCTGCACTTCAatgatg > 1:25435/1‑139 (MQ=255)
ccTTAAAAATCAGTTTGCCGGCGCCGCCTTCTGCGTCGTTACAATGGATTCGATTCCCCTCGGGCCAGAGCCAACAAGATGAGTAGCTCTTCATGGGTGAACGGCTCGCCTTCTGCCGTCCCCTg > 1:233095/1‑125 (MQ=255)
ccTTAAAAATCAGTTTGCCGGCGCCGCCTTCTGCGTCGTTACAATGGATGCGATTCCCCTCGGGCCAGAGCCAACAAGATGAGTAGCTCTTCATGGGTGAACGGCTCGCCTTCTGCCGTCCCCTg < 2:233095/125‑1 (MQ=255)
aaaaaTCAGTTTGCCGGCGCCGCCTTCTGCGTCGTTACAATGgattcgatt < 1:1291045/51‑1 (MQ=255)
aaaaaTCAGTTTGCCGGCGCCGCCTTCTGCGTCGTTACAATGgattcgatt > 2:1291045/1‑51 (MQ=255)
aTCAGTTTGCCGGCGCCGCCTTCTGCGTCGTTACAATGGATTCGATTCCCCTCGGGCCAGAGCCAACAAGATGAGTAGCTCTTCATGGGTGAACGGCTCGCCTTCTGCCGTCCCCTGCACTTCAATGATGCGCCCGTCt < 2:859344/139‑1 (MQ=255)
aGTTTGCCGGCGCCGCCTTCTGCGTCGTTACAATGGATTCGATTCCCCTCGGGCCAGAGCCAACAAGATGAGTAGCTCTTCATGGGTGAACGGCTCGCCTTCTGCCGTCCCCTGCACTTCAATGATGCGCCCGTCTTCg > 2:1529858/1‑139 (MQ=255)
aGTTTGCCGGCGCCGCCTTCTGCGTCGTTACAATGGATTCGATTCCCCTCGGGCCAGAGCCAACAAGATGAGTAGCTCTTCATGGGTGAACGGCTCGCCTTCTGCCGTCCCCTGCACTTCAATGATGCGCCCGTCTTCg > 2:390646/1‑139 (MQ=255)
gTTTGCCGGCGCCGCCTTCTGCGTCGTTACAATGGATTCGATTCCCCTCGGGCCAGAGCCAACAAGATGAGTAGCTCTTCATGGGTGAACGGCTCGCCTTCTGCCGTCCCCTGCACTTCAATGATGCGCCCGTCTTCgg < 2:1742390/139‑1 (MQ=255)
tttGCCGGCGCCGCCTTCTGCGTCGTTACAATGGATTCGATTCCCCTCGGGCCag < 2:1312089/55‑1 (MQ=255)
tttGCCGGCGCCGCCTTCTGCGTCGTTACAATGGATTCGATTCCCCTCGGGCCag > 1:1312089/1‑55 (MQ=255)
tGCCGGCGCCGCCTTCTGCGTCGTTACAATGGATTCGATTCCCCTCGGGCCAGAGCCAACAAGATGGGTAGCTCTTCATGGGTGAACGGCTCGCCTTCTGCCGTCCCCt > 2:817798/1‑109 (MQ=255)
tGCCGGCGCCGCCTTCTGCGTCGTTACAATGGATTCGATTCCCCTCGGGCCAGAGCCAACAAGATGGGTAGCTCTTCATGGGTGAACGGCTCGCCTTCTGCCGTCCCCt < 1:817798/109‑1 (MQ=255)
ccgccTTCTGCGTCGTTACAATGGATTCGATTCCCCTCGGGCCAGAGCcaa < 2:1444118/51‑1 (MQ=255)
ccgccTTCTGCGTCGTTACAATGGATTCGATTCCCCTCGGGCCAGAGCcaa > 1:1444118/1‑51 (MQ=255)
ccTTCTGCGTCGTTACAATGGATTCGATTCCCCTCGGGCCAGAGCCAACAAGATGAGTAGCTCTTCATGGGTGAACGGCTCGcc < 1:1519030/84‑1 (MQ=255)
ccTTCTGCGTCGGTACAATGGATTCGATTCCCCTCGGGCCAGAGCCAACAAGATGAGTAGCTCTTCATGGGTGAACGGCTCGcc > 2:1519030/1‑84 (MQ=255)
|
GGCGCTGATATGGTTTCATGCCTTCGCTCCTCATCTTACTTTTCTACAGACAAAAAAA‑AGGCGACTCATCAGTCGCCTTAAAAATCAGTTTGCCAGCGCCGCCTTCTGCGTCGCTACAATGGATTCGATTCCCCTCGGGCCAGAGCCAACAAGATGAGTAGCTCTTCATGGGTGAACGGCTCGCCTTCTGCCGTCCCCTGCACTTCAATGATGCGCCCGTCTTCGG > NC_000913/3815750‑3815975
|
| Alignment Legend |
|---|
Aligned base mismatch/match (shaded by quality score): ATCG/ATCG < 3 ≤ ATCG/ATCG < 15 ≤ ATCG/ATCG < 30 ≤ ATCG/ATCG < 38 ≤ ATCG/ATCG < 40 ≤ ATCG/ATCG |
Unaligned base: atcg Masked matching base: atcg Alignment gap: ‑ Deleted base: ‑ |
GATK/CNVnator alignment
N/A
