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 F13 I0 R1
|
140 |
52.5 |
2164708 |
98.8% |
2138731 |
146.1 |
Breseq alignment
BRESEQ :: Evidence
|
| evidence |
seq id |
position |
mutation |
freq |
annotation |
gene |
description |
| RA |
NC_002947_CJ‑RC |
4,158,471 |
A→C |
29.1% |
S161R (AGC→CGC) |
PP_3661 → |
membrane protein |
|
| |
seq id |
position |
ref |
new |
freq |
score (cons/poly) |
reads |
annotation |
genes |
product |
| * | NC_002947_CJ‑RC | 4,158,471 | 0 | A | C | 29.1%
| 18.5
/ 2.8
| 29 | S161R (AGC→CGC) | PP_3661 | membrane protein |
| Reads supporting (aligned to +/- strand): ref base A (11/6); new base C (5/3); total (17/12) |
| 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 |
TAGTCACCAGTACCCTGCTGATCGGCCTGTGGTGTGGCATGAAAGTGTTCAAGCTCGACCGCGATACCGCCTTGCTGACCGCCGCCGGCAGCGCCATCTGCGGCGCCGCCGCCGTGCTGGCATTCGAATCGGCGCTGCGCAGCGCCCCCCATAAAAGCGCCATGGCAGTCGGAAGCGTAGTGCTGTTCGGTACCTTGTCGATGTTCCTTTACCCACTGGCGATCAATGCCGGCTGGCTGCATCTGGATACCATGGGCGCCGGGCTGCTGCTGGGCGGCACTGTCCA > NC_002947_CJ‑RC/4158331‑4158616
|
tAGTCACCAGTACCCTGCTGATCGGCCTGTGGTGTGGCATGAAAGTGTTCAAGCTCGACCGCGATACCGCCTTGCTGACCGCCGCCGGCAGCGCCATCTGCGGCGCCGCCGCCGTGCTGGCATTCGAATCGGCGCTGCGCACCGccc > 6:202802/1‑147 (MQ=255)
cACCAGTACCCTGCTGATCGGCCTGTGGTGTGGCATGAAAGTGTTCAAGCTCGACCGCGATACCGCCTTGCTGACCGCCGCCGGCAGCGCCATCTGCGGCGCCGCCGCCGTGCTGGCATTCGAATCGGGGCGGGGCGCCGcccccc > 3:88085/1‑146 (MQ=255)
ccAGTACCCTGCTGATCGGCCTGTGGTGTGGCATGAAAGTGTTCAAGCTCGACCGCGATACCGCCTTGCTGACCGCCGCCGGCAGCGCCATCTGCGGCGCCGCCGCCGTGCTGGCATTCGAATCGGCGCGGCGCAGCGccccccca > 2:94847/1‑144 (MQ=255)
ccAGTACCCTGCTGATCGGCCTGTGGTGTGGCATGAAAGTGTTCAAGCTCGACCGCGATACCGCCTTGCTGACCGCCGCCGGCAGCGCCATCTGCGGCGCCGCCGCCGTGCTGGCATTCGAATCGGCGAGGCGCACccccccccca > 1:178047/1‑144 (MQ=255)
cAGTACCCTGCTGATCGGCCTGTGGTGTGGCATGAAAGTGTTCAAGCTCGACCGCGATACCGCCTTGCTGACCGCCGCCGGCAGCGCCATCAGCGGCGCCGCCGCCGTGCTGGCATTCGAATCGGGGCGGGCCCCCGcccccccaa > 1:249623/1‑143 (MQ=255)
aGTACCCTGCTGATCGGCCTGTGGTGTGGCATGAAAGTGTTCAAGCTCGACCGCGATACCGCCTTGCTGACCGCCGCCGGCAGCGCCATCTGCGGCGCCGCCGCCGTGCTGGCATTCGAATCGGCGCGGCGCCGCGcccccccaaa > 6:14317/1‑142 (MQ=255)
tgtggCATGAAAGTGTTCAAGCTCGACCGCGATACCGCCTTGCTGACCGCCGCCGGCAGCGCCATCTGCGGCGCCGCCGCCGTGCTGGCATTCGAATCGGGGGGGCGCCGCCCCCCCCAAAAAAAACCCAGGGGAGTCGGGAgaggt > 7:239457/1‑143 (MQ=255)
tggCATGAAAGTGTTCAAGCTCGACCGCGATACCGCCTTGCTGACCGCCGCCGGCAGCGCCATCTGCGGCGCCGCCGCCGTGCTGGCATTCGAATCGGCGCGGCGCACCCCCCCCCAAAAAAACGCCAAGGCAGTCGGGAGCGTAga > 2:42939/1‑146 (MQ=255)
cATTAATGTTTTCAAGCTCGAGGGCTATCCCGCGTTGCTGACCGCCGCCGGCTGCGCCTTTTGCGGCGCCGCCGCGGGGCGGTAATTCTATTCGGCGGTGCGCTGCGCCCCCCATAAAAGCGCCATGGCAGTCGGAAGCGTAGTGc < 2:14334/146‑1 (MQ=255)
tGAAAGTGTTCAAGCTCGACCGCGATACCGCCTTGCTGACCGCCGCCGGCAGCGCCATCTGCGGCGCCGCCGCCGTGCTGGCATTCGAATCGGCGCGGGGCCGCCCCCCCCAAAAAAGCCCCAAGGCACTAGGGACCGGAGTGATGt > 6:213926/1‑147 (MQ=255)
cgggtTCACGCTCGCCCGCTAACCCGCGGTGCTCCCGGCCGCCGGCCCCGCCAGCGGGGGCGCCGCCGCGGGGGGGGCTTTCTACGCGGCGCGGCGCAGCGCCCCCCATAAACGCGCCATGGCAGTCGGAAGCGTAGTGCTGTTCgg < 2:107021/144‑1 (MQ=255)
gACGGCTATACCGCCTTGCTGACCGCCGCCGTCAGCGCCATCTGGGGCGCCGCCGCGGTGCTGTAATTCTAATCGGCGCTGCGCAGCGCCCCCCATAAAAGCGCCATGGCAGTCGGAAGCGTAGTGCTGTTCGGTACCTTGTCGATg < 8:134895/147‑1 (MQ=255)
tgcccgccgccgGCAGCGCCATCGGCGGCGCCGCCGCGGGGCTGCCATTCCAAGCGGCGCTGCGCAGCGCCCCCCATAAAAGCGCCATGGCAGTCGGAAGCGTAGTGCTGTTCGGTACCTTGTCGATGTTCCTTTACCCACTGGCGa < 2:115318/144‑1 (MQ=255)
tccccggcgcggGCTGCGCATTCTGGGGGGCCGCCGCGGTGCTGGAATTCTTTTCGGCGCTGGGCTGCGCCCCCCATAAAAGCGCCATGGCAGTCGGAAGCGTAGTGCTGTTCGGTACCTTGTCGATGTTCCTTTACCCACTGGCGa < 4:8860/144‑1 (MQ=255)
gcgcCATCTGCGGCGCCGCCGCCGTGCTGGCATTCGAATCGGCGCAGCGCAGCGCCCCCCAAAAAAACGCCATGGCAGTCGGAAGCGTATTGCTGTTCGGTAACATGTCGATTTTACATTTACCACAGGCGCTAAATGCCagcaggc > 6:254872/1‑147 (MQ=255)
aTCTGCGGCGCCGCCGCCGTGCTGGCATTCTAATCGGCGCTGCGCAGCGCCCCCCATAAAAGCGCCATGGCAGTCGGAAGCGTAGTGCTGTTCGGTACCTTGTCGATGTTCCTTTACCCACTGGCGATCAATGCCGGCTGGCTGCAt < 8:117721/147‑1 (MQ=255)
cggcgccgcggTGCTGGAATTCGCCGCGGCGCGCCCCCCCCCCCCCCATAAAAGCGCCATGGCAGTCGGAAGCGTAGTGCTGTTCGGTACCTTGTCGATGTTCCTTTACCCACTGGCGATCAATGCCGGCTGGCTGCATCTGGATAc < 1:180816/144‑1 (MQ=255)
cgccggcgGGCTTGCATTTCAATCGGCGCGGCGCCCCGCCCCCCATAAAAGCGCCATGGCAGTCGGAAGCGTAGTGCTGTTCGGTACCTTGTCGATGTTCCTTTACCCACTGGCGATCAATGCCGGCTGGCTGCATCTGGATACCAt < 8:251123/147‑1 (MQ=255)
ccgccgTGCTGGCATTCGAATCGGCGCTGCGCCGCGGCCCCCATAAAAGCCCCATGGCACTCGGGAGCGGAGGGCAGTTCGGTACCGTGTCGCAGGTCCGTTACCCCCTGGCCAACAATGCCGGCGGGCTGCATGGGGATTCCATgg > 2:50531/1‑147 (MQ=255)
ccgTGCTGGCATTCGAATCGGCGCGGCGCAGCCCCCCCCATAAAAGCGCCATGGCAGTCGGAAGCGTAGTGCTGTTCGGTACCTTGTCGATGTTCCTTTACCCACTGGCGATCAATGCCGGCTGGCTGCATCTGGATACCATGGgcg < 6:216178/147‑1 (MQ=255)
cgTGGTGGCTTTCTAATGGGCTGTGCGCTGGGCCCCCCATAAAAGCGCCATGGCAGTCGGAAGCGTAGTGCTGTTCGGTACCTTGTCGATGTTCCTTTACCCACTGGCGATCAATGCCGGCTGGCTGCATCTGGATACCATGGgcgc < 2:178047/147‑1 (MQ=255)
cTGGCATTCGAATCGGCGCTGCGCAGCGCCCCCCAAAAAAACGCCAAGGCAGTAGGAAGCGTAGTGCTGTTAGGTAACATGTAGATTTTACATTTACCACTGGCGCTAAATTCCGGCGGGCGGCATATGGATACAAATGGCGCCcgg > 8:137046/1‑147 (MQ=255)
cTGGCATTCGAATCGGCGCGGCGCAGCGCCCCCCATAAAAGCGGCATGGCAGTCGGGAGCGTAGTGGGGTTGGGTTCCGTGTGGCTGTTGCTTTACCCACTGGCGATAAATGCCGGCTGGCGGGCTCTGGTTTCCATGGGCGCCggg > 6:181872/1‑147 (MQ=255)
cTGGCATTCGAATCGGCGCGGCCCAGCGCCCCCCATAAAAGCACCATGGCAGTCGGAACCGGAGTGCTGTTCGGTACCGTGTCGCAGTTACATTTCCCACAGTCGAAAAATTCCCCCAGGCAGGATCAGCATAACAAGGGCGccccg > 2:227037/1‑144 (MQ=255)
cTGCCATTCCACGCGGCGCGGCCCCCCCCCCCCCATAAAAGCGCCATGGCAGTCGGAAGCGTAGTGCTGTTCGGTACCTTGTCGATGTTCCTTTACCCACTGGCGATCAATGCCGGCTGGCTGCATCTGGATACCATGGGCGCCggg < 5:14317/147‑1 (MQ=255)
cGGCGCTGCGCAGCGCCCCCCATAAAAGCGCCATGGCAGTCGGAAGCGTAGTGCTGTTCGGTACCTTGTCGATGTTCCTTTACCCACTGGCGATCAATGCCGGCTGGCTGCATCTGGATACCATGGGCGCCGGGCTGCTGCTGggcg < 6:255579/147‑1 (MQ=255)
cgcTGCGCAGCGCCCCCCATAAAAGCGCCATGGCAGTCGGAAGCGTAGTGCTGTTCGGTACCTTGTCGATGTTCCTTTACCCACTGGCGATCAATGCCGGCTGGCTGCATCTGGATACCATGGGCGCCGGGCTGCTGCTGGGCGGCa > 5:195897/1‑147 (MQ=255)
cAGCGCCCCCCATAAAAGCGCCATGGCAGTCGGAAGCGTAGTGCTGTTCGGTACCTTGTCGATGTTCCTTTACCCACTGGCGATCAATGCCGGCTGGCTGCATCTGGATACCATGGGCGCCGGGCTGCTGCTGGGCGGCACTGTCCa > 4:262933/1‑147 (MQ=255)
cAGCGCCCCCCATAAAAGCGCCATGGCAGTCGGAAGCGTAGTGCTGATCGGTACCTTGTCGATGTTCCTTTACCCACTGGCGATCAATGCCGGCTGGCTGCATCTGGATACCATGGGCGCCGGGCTGCTGCTGGGCGGCACTGTCCa > 1:54482/1‑147 (MQ=255)
|
TAGTCACCAGTACCCTGCTGATCGGCCTGTGGTGTGGCATGAAAGTGTTCAAGCTCGACCGCGATACCGCCTTGCTGACCGCCGCCGGCAGCGCCATCTGCGGCGCCGCCGCCGTGCTGGCATTCGAATCGGCGCTGCGCAGCGCCCCCCATAAAAGCGCCATGGCAGTCGGAAGCGTAGTGCTGTTCGGTACCTTGTCGATGTTCCTTTACCCACTGGCGATCAATGCCGGCTGGCTGCATCTGGATACCATGGGCGCCGGGCTGCTGCTGGGCGGCACTGTCCA > NC_002947_CJ‑RC/4158331‑4158616
|
| Alignment Legend |
|---|
Aligned base mismatch/match (shaded by quality score): ATCG/ATCG < 3 ≤ ATCG/ATCG < 14 ≤ ATCG/ATCG < 15 ≤ ATCG/ATCG < 27 ≤ ATCG/ATCG < 36 ≤ ATCG/ATCG |
Unaligned base: atcg Masked matching base: atcg Alignment gap: ‑ Deleted base: ‑ |
GATK/CNVnator alignment
N/A
