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 |
|
A5 F13 I0 R1
|
213 |
60.4 |
2554362 |
98.6% |
2518600 |
147.1 |
Breseq alignment
BRESEQ :: Evidence
|
| evidence |
seq id |
position |
mutation |
freq |
annotation |
gene |
description |
| RA |
NC_002947_CJ‑RC |
4,158,466 |
T→G |
47.8% |
L159R (CTG→CGG) |
PP_3661 → |
membrane protein |
|
| |
seq id |
position |
ref |
new |
freq |
score (cons/poly) |
reads |
annotation |
genes |
product |
| * | NC_002947_CJ‑RC | 4,158,466 | 0 | T | G | 47.8%
| 10.6
/ 27.0
| 27 | L159R (CTG→CGG) | PP_3661 | membrane protein |
| Reads supporting (aligned to +/- strand): ref base T (8/4); new base G (7/6); total (17/10) |
| Fisher's exact test for biased strand distribution p-value = 6.88e-01 |
| Kolmogorov-Smirnov test that lower quality scores support variant p-value = 1.43e-02 |
TGTCGGTGCTGGTAGTCACCAGTACCCTGCTGATCGGCCTGTGGTGTGGCATGAAAGTGTTCAAGCTCGACCGCGATACCGCCTTGCTGACCGCCGCCGGCAGCGCCATCTGCGGCGCCGCCGCCGTGCTGGCATTCGAATC‑GGCGCTGCGCAGCGCCCCCCATAAAAGCGCCATGGCAGTCGGAAGCGTAGTGCTGTTCGGTACCTTGTCGATGTTCCTTTACCCACTGGCGATCAATGCCGGCTGGCTGCATCTGGATACCATGGGCGCCGGGCTGCTGCTGGGCGGCACTG > NC_002947_CJ‑RC/4158319‑4158612
|
tgtCGGTGCTGGTAGTCACCAGTACCCTGCTGATCGGCCTGTGGTGTGGCATGAAAGTGTTCAAGCTCGACCGCGATACCGCCTTGCTGACCGCCGCCGGCAGCGCCATCTGCGGCGCCGCCGCCGTGCTGGCATTCGAATC‑GGCGCTg < 2:115652/149‑1 (MQ=255)
tGCTGGTAGTCACCAGTACCCTGCTGATCGGCCTGTGGTGTGGCATGAAAGTGTTCAAGCTCGACCGCGATACCGCCTTGCTGACCGCCGCCGGCAGCGCCATCTGCGGCGCCGCCGCCGTGCTGGCATTCGAATC‑GGCGCTGCGCAgc < 3:44111/149‑1 (MQ=255)
cTGGTAGTCACCAGTACCCTGCTGATCGGCCTGTGGTGTGGCATGAAAGTGTTCAAGCTCGACCGCGATACCGCCTTGCTGACCGCCGCCGGCAGCGCCATCTGCGGCGCCGCCGCCGTGCTGGCATTCGAATC‑GGCGCTGCGCAgcgc < 7:283168/149‑1 (MQ=255)
gTCACCAGTACCCTGCTGATCGGCCTGTGGTGTGGCATGAAAGTGTTCAAGCTCGACCGCGATACCGCCTTGCTGACCGCCGCCGGCAGCGCCATCTGCGGCGCCGCCGCCGTGCTGGCATTCGAATC‑GGGGGGGGGGCGCGccccccc > 3:74209/1‑148 (MQ=255)
tCACCAGTACCCTGCTGATCGGCCTGTGGTGTGGCATGAAAGTGTTCAAGCTCGACCGCGATACCGCCTTGCTGACCGCCGCCGGCAGCGCCATCTGCGGCGCCGCCGCCGTGCTGGCATTCGAATC‑GGGGGGGCGCCGccccccccc > 1:229686/1‑147 (MQ=255)
ccccTGCTCATCGGCCTGGGGTGGGGCATCAAAGTGTTCACGCTCGCCCGCTATACCGCCTTGCTCACCGCCGCCGGCAGCGCCATGTGCGGCGCCGCCGCCGTGCGGGCATTCTAATC‑GGCGCGGCGCAGCGCCCCCCATAAAAgcgc < 8:239060/148‑1 (MQ=255)
cccTGCTGATCGGCCTGTGGTGTGGCATGAAAGTGTTCAAGCTCGACCGCGATACCGCCTTGCTGACCGCCGCCGGCAGCGCCATCTGCGGCGCCGCCGCCGTGCTGGCATTCGAATC‑GGGGGGGCGCCGCCCCCCCCCAaaaaaaac > 3:252863/1‑144 (MQ=255)
ccTGCTGATCGGCCTGTGGTGTGGCATGAAAGTGTTCAAGCTCGACCGCGATACCGCCTTGCTGACCGCCGCCGGCAGCGCCATCTGCGGCGCCGCCGCCGTGCTGGCATTCGAATC‑GGGGCGGGGCCGCGCCCCCCCAaaaaaaaac > 3:265702/1‑143 (MQ=255)
ccTGCTGATCGGCCTGTGGTGTGGCATGAAAGTGTTCAAGCTCGACCGCGATACCGCCTTGCTGACCGCCGCCGGCAGCGCCATCTGCGGCGCCGCCGCCGTGCTGGCATTCGAATC‑GGCGCGGCGCACCCCCCCCCCAaaaaaaccc > 1:84118/1‑143 (MQ=255)
ccTGCTGATCGGCCTGTGGTGTGGCATGAAAGTGTTCAAGCTCGACCGCGATACAGCCTTGCTGACCGCCGCCGGCAGCGCCATCTGCGGCGCCGCCGCCGTGCTGGCATTCGAATCGGGCCGTGCCCGCCGCCCCCCAAAAACCCGcc > 4:123498/1‑149 (MQ=255)
ctgctgCGCGGCGTGGGGTGGGGCATGACTGTGTCCCCGCGCGGCCGCGAACCCGCCGTGCCCCCCGCCGCCGGCCGCGCCCGCGGCGGCGCCGCCGCGGTGCGGGCATCCGACGC‑GGCGCGGCGCCGCGCCCCCCATAAAAGCGCCAt < 8:199316/149‑1 (MQ=255)
tgctgATCGGCCTGTGGTGTGGCATGAAAGTGTTCAAGCTCGACCGCGATACCGCCTTGCTGACCGCCGCCGGCAGCGCCATCTGCGGCGCCGCCGCCGTGCTGGCATTCGAATC‑GGCGCTGCGCAGCGCCCCCCCAAAAAAAGCCaag > 1:203889/1‑147 (MQ=255)
tgATCGGCCTGTGGTGTGGCATGAAAGTGTTCAAGCTCGACCGCGATACCGCCTTGCTGACCGCCGCCGGCAGCGCCATCTGCGGCGCCGCCGCCGTGCTGGCATTCGAATC‑GGGGCGGCGCACCGCCCCCCAAAAAAACGCCATgg > 6:163248/1‑147 (MQ=255)
gCCTGTGGTGTGGCATGAAAGTGTTCAAGCTCGACCGCGATACCGCCTTGCTGACCGCCGCCGGCAGCGCCATCTGCGGCGCCGCCGCCGTGCTGGCATTCGAATC‑GGCGCAGCGCAGCCCCCCCCAAAAAAACCCCATCGCAGTccg > 6:249412/1‑146 (MQ=255)
cAAGCTCGACCGCGATACCGCCTTGCTGACCGCCGCCGGCAGCGCCATCTGCGGCGCCGCCGCCGTGCTGGCATTCGAATC‑GGCGCGGGGCAGCGCCCCCCCAAAAATCGCCAACTCAGTACGCAGCGGAGTGGGGTTGTGTAGCTTGt > 7:186258/1‑149 (MQ=255)
cAAGCGCGCCCGCTAACCCGCCTTGCTGCCCGCCGCCGGCAGCGCCATCTGGGGCGCCGCCGCGGGGGGGGCATTCTAATC‑GGCGCGGCGCAGCGCCCCCCATAAAAGCGCCATGGCAGTCGGAAGCGTAGTGCTGTTCGGTACCTTGt < 8:271671/149‑1 (MQ=255)
ccGCGATACCGCCTTGCTGACCGCCGCCGGCAGCGCCATCTGCGGCGCCGCCGCCGTGCTGGCATTCGAATC‑GGCGCAGCGCCCCGCCCCCCCCAAAAAAGCCCAGGCCCGCGGGAGCGGAGTGGGGTTGGGTACCGTGTCggggttg > 5:238680/1‑142 (MQ=255)
gATACCGCCTTGCTGACCGCCGCCGGCAGCGCCATCTGCGGCGCCGCCGCCGTGCTGGCATTCGAATC‑GGCGCTGCGCCGCGCCCCCCCAAAAAACGCCATGGCAGTCGGAAGCGGAGTGCGGTTCGGTACCATTTGGATGttgcgtt > 8:61018/1‑143 (MQ=255)
cccccgGCAGCGCCTTCGGCGGCGCCGCCGCGGTGCTGGCATTCGAAGC‑GGCGGGCCTCCGCGCCCCCCATAAAAGCGCCATGGCAGTCGGAAGCGTAGTGCTGTTCGGTACCTTGTCGATGTTCCTTTACCCACTGGCGATCAATGcc < 8:37803/146‑1 (MQ=255)
ccttCTGCGGCGCCGCCGCCGTGCTGGCATTCGAAGC‑GGCGCGGCGCAGCGCCCCCCATAAAAGCGCCATGGCAGTCGGAAGCGTAGTGCTGTTCGGTACCTTGTCGATGTTCCTTTACCCACTGGCGATCAATGCCGGCTGGCTGCAt < 2:84118/146‑1 (MQ=255)
gcggcgCCGCCGCCGGGCTGGCATTCCACGC‑GGCGCTGCGCAGCGCCCCCCATAAAAGCGCCATGGCAGTCGGAAGCGTAGTGCTGTTCGGTACCTTGTCGATGTTCCTTTACCCACTGGCGATCAATGCCGGCTGGCTGCATCTGGAt < 4:74209/149‑1 (MQ=255)
ggcgCCGCCGCCGTGCTGGCATTCGAATC‑GGCGCTGCGCAGCGCCCCCCATAAAAGCGCCATGGCAGTGCGAAGCGTAGTGCTGTTAGGGACCATGTCGATGTTGCATTACCCACAGGCGATCAAATCCGGCGGGCTGCATCTGGGTaa > 6:154716/1‑148 (MQ=255)
ggCATTCGAAGC‑GGCGCGGGGCCGCGCCCCCCATAAAAGCGCCATGGCAGTCGGAAGCGTAGTGCTGTTCGGTACCTTGTCGATGTTCCTTTACCCACTGGCGATCAATGCCGGCTGGCTGCATCTGGATACCATGGGCGCCGGgctgc < 2:229686/149‑1 (MQ=255)
gcgcTGCGCAGCGCCCCCCATAAAAGCGCCATGGCAGTCGGAAGCGTAGTGCTGTTCGGTACCTTGTCGATGTTCCTTTACCCACTGGCGATCAATGCCGGCTGGCTGCATCTGGATACCATGGGCGCCGGGCTGCTGCTGGGCGGCAc > 2:181321/1‑149 (MQ=255)
gcgcTGCGCAGCGCCCCCCATAAAAGCGCCATGGCAGTCGGAAGCGTAGTGCTGTTCGGTACCTTGTCGATGTTCCTTTACCCACTGGCGATCAATGCCGGCTGGCTGCATCTGGATACCATGGGCGCCGGGCTGCTGCTGGGCGGCAc > 1:135211/1‑149 (MQ=255)
gcTGCGCAGCGCCCCCCATAAAAGCGCCATGGCAGTCGGAAGCGTAGTGCTGTTCGGTACCTTGTCGATGTTCCTTTACCCACTGGCGATCAATGCCGGCTGGCTGCATCTGGATACCATGGGCGCCGGGCTGCTGCTGGGCGGCACTg > 2:38455/1‑149 (MQ=255)
gcTGCGCAGCGCCCCCCATAAAAGCGCCATGGCAGTCGGAAGCGTAGTGCTGTTCGGTACCTTGTCGATGTTCCTTTACCCACTGGCGATCAATGCCGGCTGGCTGCATCTGGATACCATGGGCGCCGGGCTGCTGCTGGGCGGCACTg > 2:33602/1‑149 (MQ=255)
|
TGTCGGTGCTGGTAGTCACCAGTACCCTGCTGATCGGCCTGTGGTGTGGCATGAAAGTGTTCAAGCTCGACCGCGATACCGCCTTGCTGACCGCCGCCGGCAGCGCCATCTGCGGCGCCGCCGCCGTGCTGGCATTCGAATC‑GGCGCTGCGCAGCGCCCCCCATAAAAGCGCCATGGCAGTCGGAAGCGTAGTGCTGTTCGGTACCTTGTCGATGTTCCTTTACCCACTGGCGATCAATGCCGGCTGGCTGCATCTGGATACCATGGGCGCCGGGCTGCTGCTGGGCGGCACTG > NC_002947_CJ‑RC/4158319‑4158612
|
| Alignment Legend |
|---|
Aligned base mismatch/match (shaded by quality score): ATCG/ATCG < 3 ≤ ATCG/ATCG < 14 ≤ ATCG/ATCG < 15 ≤ ATCG/ATCG < 32 ≤ ATCG/ATCG < 36 ≤ ATCG/ATCG |
Unaligned base: atcg Masked matching base: atcg Alignment gap: ‑ Deleted base: ‑ |
GATK/CNVnator alignment
N/A
