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 |
|
A3 F14 I0 R1
|
206 |
76.7 |
3255580 |
98.8% |
3216513 |
146.3 |
Breseq alignment
BRESEQ :: Evidence
|
| evidence |
seq id |
position |
mutation |
freq |
annotation |
gene |
description |
| RA |
NC_002947_CJ‑RC |
4,158,471 |
A→C |
55.1% |
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 | 55.1%
| ‑5.4
/ 14.3
| 31 | S161R (AGC→CGC) | PP_3661 | membrane protein |
| Reads supporting (aligned to +/- strand): ref base A (4/10); new base C (9/8); total (13/18) |
| Fisher's exact test for biased strand distribution p-value = 2.75e-01 |
| Kolmogorov-Smirnov test that lower quality scores support variant p-value = 7.31e-01 |
ACCAGTACCCTGCTGATCGGCCTGTGGTGTGGCATGAAAGTGTTCAAGCTCGACCGCGATACCGCCTTGCTGACCGCCGCCGGCAGCGCCATCTGCGGCGCCGCCGCCGTGCTGGCATTCGAATCGGCGCTGCGCAGCGCCCCCCATAAAAGCGCCATGGCAGTCGGAAGCGTAGTGCTGTTCGGTACCTTGTCGATGTTCCTTTACCCACTGGCGATCAATGCCGGCTGGCTGCATCTGGATACCATG > NC_002947_CJ‑RC/4158336‑4158584
|
aCCAGTACCCTGCTGATCGGCCTGTGGTGTGGCATGAAAGTGTTCAAGCTCGACCGCGATACCGCCTTGCTGACCGCCGCCGGCAGCGCCATCTGCGGCGCCGCCGCCGTGCTGGCATTCGAATCGGCGCGGCGGCGCGcccccccca > 1:69331/1‑145 (MQ=255)
cAGTACCCTGCTGATCGGCCTGTGGTGTGGCATGAAAGTGTTCAAGCTCGACCGCGATACCGCCTTGCTGACCGCCGCCGGCAGCGCCATCTGCGGCGCCGCCGCCGTGCTGGCATTCGAATCGGCGCTGCGCAGCGCCCCCCAaaaa > 1:310913/1‑148 (MQ=255)
gTACCCTGCTGATCGGCCTGTGGTGTGGCATGAAAGTGTTCAAGCTCGACCGCGATACCGCCTTGCTGACCGCCGCCGGCAGCGCCATCTGCGGCGCCGCCGCCGTGCTGGCATTCGAATCGGGGCGGAGCCCCGCCCCCCCAaaaaa > 2:349916/1‑147 (MQ=255)
gTACCCTGCTGATCGGCCTGTGGTGTGGCATGAAAGTGTTCAAGCTCGACCGCGATACCGCCTTGCTGACCGCCGCCGGCAGCGCCATCTGCGGCGCCGCCGCCGTGCTGGCATTCGAATCGGCGCGGCGCCCCGCCCCCCCCaaaaac > 3:326203/1‑147 (MQ=255)
tACCCTGCTGATCGGCCTGTGGTGTGGCATGAAAGTGTTCAAGCTCGACCGCGATACCGCCTTGCTGACCGCCGCCGGCAGCGCCATCTGCGGCGCCGCCGCCGTGCTGGCATTCGAATCGGGGCTGCGCCGCGCCCCCCCAAAAAacg > 2:287770/1‑149 (MQ=255)
tACCCGGCTGATCGGCCTGTGGTGTGGCATAAAATTTTCCAAGCTCGCCCGCTAAACCGCCTTGCTCACCGCCGCCGGCAGCGCAATCTGCGGCGCCGCCGCCGGGCTGCAATTCGAATCGGCGCTGCGCAGCGCCTCCCATAAAAgc < 2:198420/148‑1 (MQ=255)
tgctgATCGGCCTGTGGTGTGGCATGAAAGTGTTCAAGCTCGACCGCGATACCGCCTTGCTGACCGCCGCCGGCAGCGCCATCTGCGGCGCCGCCGCCGTGCTGGCATTCGAATCGGCGCGGCGCCCCCCCCCCCaaaaaaaacccaa > 5:159700/1‑141 (MQ=255)
tCGGCCTGTGGTGTGGCATGAAAGTGTTCAAGCTCGACCGCGATACCGCCTTGCTGACCGCCGCCGGCAGCGCCATCTGCGGCGCCGCCGCCGTGCTGGCATTCGAATCGGCGCGGCGCCGCGCCCCCCAAAAAAGCGCCCTGGCAGt > 6:332979/1‑148 (MQ=255)
ccTGGGGGGTGGCATTAATGTGTTCACGCGCGCCCGCGAACCCGCCTTGCTGCCCGCCGCGGGCAGCGCCTTCTGCGGCGCCGCCGCCGTGCTGGCATTCTAATCGGCGCTGCGCCGCGCCCCCCATAAAAGCGCCATGGCAGTCGGaa < 4:326203/149‑1 (MQ=255)
tgtggtgtggCATGAAAGTGTTCAAGCTCGACCGCGATACCGCCTTGCTGACCGCCGCCGGCAGCGCCATCTGCGGCGCCGCCGCCGTGCTGGCATTCGAATCGGCGCGGCGCCGCGCCCCCCCCAAAAGCCCCAAGGCAGTGGGCAg > 5:196544/1‑148 (MQ=255)
gCATGAATTTGTTCAAGCTCGACCGCTATACCGCCTTGCTTACCGCCGCCGTCTGCGCCAGCTGGGGCGCCGCCGCGGTTGTGGCATTCGACTCGGCGCTGCGCAGCGCCCCCCATAAAAGCGCCATGGCAGTCGGAAGCGTAGTGCt < 2:237762/148‑1 (MQ=255)
aaTGAAAGTGTTCATGCTCGACCGCTATACCGCCTTGCTGACCGCCGCCGGCAGCGCCATCTGCGGCGCCGCCGCCGGGCGGGAATTCGAATCGGCGCTGCGCAGCGCCCCCCATAAAAGCGCCATGGCAGTCGGAAGCGTAGTGCTGt < 4:28915/148‑1 (MQ=255)
aaaGTGTTCAAGCTCGACCGCGATACCGCCTTGCTGACCGCCGCCGGCAGCGCCATCTGCGGGGCCGCCACGGTGGGGGATTTCTAATCGGGGCTGGGCAGCGCCCCCCATAAAAGCGCCATGGCAGTCGGAAGCGTAGTGCTGTTCg < 8:294006/148‑1 (MQ=255)
cGACCGCGATACTGCCTTGCTGACCGCCGCCGGCAGCGCCATCTGCGGCGCCGCCGCCGTGCTGGCATTCGAATCGGCGCTGCGCACCGCCCCCCAGAAAAGCGCCAAGGCCGTCGGAAGCGGAGTGGTGTTCGGTGCCTTGGCGATg > 8:411440/1‑148 (MQ=255)
cGACCGCGATACCGCCTTGCTGCCCGCCGCCGGCCGCGCCATCTGCGGCGCCGCCGCGGTGCTGGCATTCTAATCGGCGCTGCGCAGCGCCCCCCATAAAAGCGCCATGGCAGTCGGAAGCGTAGTGCTGTTCGGTACCTTGTCGATg < 6:234661/148‑1 (MQ=255)
ccGCGATACCGCCTTGCTGACCGCCGCCGGCAGCGCCATCTGCGGCGCCGCCGCCGTGCTGGCATTCGAATCGGGGCTGCGCAGCGCCCCCCAAAAAAACGCCAAAGCAGTACGAATCCTAGAGCAGTTAGGTAACATGTGGAtttt > 6:302859/1‑147 (MQ=255)
cGCCTTGCTGACCGCCGCCGGCAGCGCCATCTGCGGCGCCGCCGCCGTGCTGGCATTCGAATCGGCGCTGCGCAGCTCCCCCCATAAAAGCGCCATGGCAGTCGGAAGCGTAGTGCTGTTCGGTACCTTGTCGATGTTCCTTTACCCAc < 2:264949/149‑1 (MQ=255)
ccTTGCTCCCCCCCCCCGCCCGCGCCAGCGGCGGCGCCGCCGCGGGGCTGCAATTCCACGCGGCGCGGCGCCGCCCCCCCCATAAAAGCGCCATGGCAGTCGGAAGCGTAGTGCTGTTCGGTACCTTGTCGATGTTCCTTTACCCACt < 6:144398/148‑1 (MQ=255)
cTGCCCGCCGCGGGCTGCGCCATCGGGGGCGCCGCCGCGGTGGTGGCTTTCTATGCGGCGGGGCGCCGCCCCCCCCATAAAAGCGCCATGGCAGTCGGAAGCGTAGTGCTGTTCGGTACCTTGTCGATGTTCCTTTACCCACTGGCGa < 6:24346/148‑1 (MQ=255)
tGACCGCCGCCGGCAGCGCCATCTGCGGCGCCGCCGCCGTGCTGGCATTCGAATCGGGGCGGCGCCGCGCCCCCCCAAAAAACGCCCAGGGAGTGGGGAGGGGAGTGGGGTTGGGTTGCGTGTGGGTGTTGGTTTTCCCACAgggggt > 2:9500/1‑144 (MQ=255)
ccgccgccgGCAGCGCCATCTGCGGCGCCGCCGCCGTGCTGGCATTCGAATCGGGGCGGCGCCCCGCCCCCCCAAAAAACGCCCTGGCAGTCGGAAGCGGAGTGGTGTTGGGGAACGTGTGGTAGTTGGTTTTACCACAGGCGAtga > 8:358929/1‑145 (MQ=255)
ccgGCCGCGCCTTCGGGGGCGCCGCCGCGGTGCTGTCATTCTACTGGGGGCTGCCCCGCCCCCCCCATAAAAGCGCCATGGCAGTCGGAAGCGTAGTGCTGTTCGGTACCTTGTCGATGTTCCTTTACCCACTGGCGATCAATGCCggc < 1:349916/149‑1 (MQ=255)
aGCGCCATCTGCGGCGCCGGCGCCGGGCTGGAATTGGACTGGGCGGGGGGCAGCGCCCCCCATAAAAGCGCCATGGCAGTCGGAAGCGTAGTGCTGTTCGGTACCTTGTCGATGTTCCTTTACCCACTGGCGATCAATGCCggctggct < 4:212566/149‑1 (MQ=255)
aGCGCCATCTGCGGCGCCGCCGCCGTCCCGCCATTCGAATCGCCGCTGCGCAGCGCCCCCCATAAAAGCGCCATGCCAGTCGGAAGCGTAGTGCTGTTCGGTACCTTGTCGATGTTCCTTTACCCACTGGCGATCAATGCCggctggct < 2:310913/149‑1 (MQ=255)
gcCCTCGGCGGCGCCGCCGGCGTGCTTGATTGCCTCGCGGGGGGGCGCCCCCCCCCCCATAAAAGCGCCATGGCAGTCGGAAGCGTAGTGCTGTTCGGTACCTTGTCGATGTGCCTTTACCCACTGGCGATCAATGCCGGCTGGCTGCa < 3:109966/149‑1 (MQ=255)
ccATGTGCGGCGCCGCCGCGGGGCTGGCATTCGAAGCGGCGCGGCGAAGCCCCCCCCATAAAAGCGCCATGGCAGTCGGAAGCGTAGTGCTGTTCGGTACCTTGTCGATGTTCCTTTACCCACTGGCGATCAATGCCGGCTGGCTGCAt < 4:240142/149‑1 (MQ=255)
gggcggcgCCGCCGCGGTGCTGTAATTCTATGCGGCGCTGCGCCGCGCCCCCCATAAAAGCGCCATGGCAGTCGGAAGCGTAGTGCTGTTCGGTACCTTGTCGATGTTCCTTTACCCACTGGCGATCAATGCCGGCTGGCTGCATCTg < 2:73326/146‑1 (MQ=255)
cggcggcgCCGCCGGCGTGGGGGAATTCGACGCGGCGCGGCGCCCCCCCCCCCATAAAAGCGCCATGGCAGTCGGAAGCGTAGTGCTGTTCGGTACCTTGTCGATGTTCCTTTACCCACTGGCGATCAATGCCGGCTGGCTGCATCTg < 5:258989/146‑1 (MQ=255)
ggcggcgCCGCCGCCGGGCTGCCATTCGACGCGGCGCGGCGCCGCCCCCCCCATAAAAGCGCCATGGCAGTCGGAAGCGTAGTGCTGTTCGGTACCTTGTCGATGTTCCTTTACCCACTGGCGATCAATGCCGGCTGGCTGCATCTGGa < 3:336309/148‑1 (MQ=255)
ccgccgcggGGGTGGAATTCTAATCGGCGCTGCGCAGCGCCCCCCATAAAAGCGCCATGGCAGTCGGAAGCGTAGTGCTGTTCGGTACCTTGTCGATGTTCCTTTACCCACTGGCGATCAATGCCGGCTGGCTGCATCTGGATACCATg < 2:69331/149‑1 (MQ=255)
tCGGCGCTGCGCAGCGCCCCCCATAAAAGCGCCATGGCAGTCGGAAGCGGAGTGCTGTTAGGTACCTTGTCGATGTTGCTTTAACCACTGGCGATCAATTCCg > 7:247247/1‑103 (MQ=255)
|
ACCAGTACCCTGCTGATCGGCCTGTGGTGTGGCATGAAAGTGTTCAAGCTCGACCGCGATACCGCCTTGCTGACCGCCGCCGGCAGCGCCATCTGCGGCGCCGCCGCCGTGCTGGCATTCGAATCGGCGCTGCGCAGCGCCCCCCATAAAAGCGCCATGGCAGTCGGAAGCGTAGTGCTGTTCGGTACCTTGTCGATGTTCCTTTACCCACTGGCGATCAATGCCGGCTGGCTGCATCTGGATACCATG > NC_002947_CJ‑RC/4158336‑4158584
|
| Alignment Legend |
|---|
Aligned base mismatch/match (shaded by quality score): ATCG/ATCG < 3 ≤ ATCG/ATCG < 14 ≤ ATCG/ATCG < 15 ≤ ATCG/ATCG < 21 ≤ ATCG/ATCG < 36 ≤ ATCG/ATCG |
Unaligned base: atcg Masked matching base: atcg Alignment gap: ‑ Deleted base: ‑ |
GATK/CNVnator alignment
N/A
