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 |
|
A1 F14 I0 R1
|
248 |
61.6 |
2601574 |
98.7% |
2567753 |
146.9 |
Breseq alignment
BRESEQ :: Evidence
|
| evidence |
seq id |
position |
mutation |
freq |
annotation |
gene |
description |
| RA |
NC_002947_CJ‑RC |
4,158,471 |
A→C |
38.3% |
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 | 38.3%
| ‑1.3
/ 4.5
| 21 | S161R (AGC→CGC) | PP_3661 | membrane protein |
| Reads supporting (aligned to +/- strand): ref base A (5/7); new base C (5/3); total (10/11) |
| Fisher's exact test for biased strand distribution p-value = 6.50e-01 |
| Kolmogorov-Smirnov test that lower quality scores support variant p-value = 8.61e-01 |
GGTGCTGGTAGTCACCAGTACCCTGCTGATCGGCCTGTGGTGTGGCATGAAAGTGTTCAAGCTCGACCGCGATACCGCCTTGCTGACCGCCGCCGGCAGCGCCATCTGCGGCGCCGCCGCCGTGCTGGCATTCGAATCGGCGCTGCGCAGCGCCCCCCATAAAAGCGCCATGGCAGTCGGAAGCGTAGTGCTGTTCGGTACCTTGTCGATGTTCCTTTACCCACTGGCGATCAATGCCGGCTGGCTGCATCTGGATACCATGGGCGCCGGGCTGCTGC > NC_002947_CJ‑RC/4158323‑4158600
|
ggTGCTGGTAGTCACCAGTACCCTGCTGATCGGCCTGTGGTGTGGCATGAAAGTGTTCAAGCTCGACCGCGATACCGCCTTGCTGACCGCCGCCGGCAGCGCCATCTGCGGCGCCGCCGCCGTGCTGGCATTCGAATCGGCGCTGCGCa < 4:113395/149‑1 (MQ=255)
tGGTAGTCACCAGTACCCTGCTGATCGGCCTGTGGTGTGGCATGAAAGTGTTCAAGCTCGACCGCGATACCGCCTTGCTGACCGCCGCCGGCAGCGCCATCTGCGGCGCCGCCGCCGTGCTGGCATTCGAATCGGCGCGGCGCAGCGcc > 8:80713/1‑149 (MQ=255)
tCACCAGTACCCTGCTGATCGGCCTGTGGTGTGGCATGAAAGTGTTCAAGCTCGACCGCGATACCGCCTTGCTGACCGCCGCCGGCAGCGCCATCTGCGGCGCCGCCGCCGTGCTGGCATTCGAATCGGGGCGGGGCCGCGccccccc > 4:120125/1‑147 (MQ=255)
aCCAGTACCCTGCTGATCGGCCTGTGGTGTGGCATGAAAGTGTTCAAGCTCGACCGCGATACCGCCTTGCTGACCGCCGCCGGCAGCGCCATCTGCGGCGCCGCCGCCGTGCTGGCATTCGAATCGGGGCGGGGCCCCGcccccccca > 5:96936/1‑145 (MQ=255)
ccAGTACCCTGCTGATCGGCCTGTGGTGTGGCATGAAAGTGTTCAAGCTCGACCGCGATACCGCCTTGCTGACCGCCGCCGGCAGCGCCATCTGCGGCGCCGCCGCCGTGCTGGCATTCGAATCGGGGCGGCCCCGCGccccccccaa > 1:169958/1‑144 (MQ=255)
ccTGCTGATCGGCCTGTGGTGTGGCATGAAAGTGTTCAAGCTCGACCGCGATACCGCCTTGCTGACCGCCGCCGGCAGCGCCATCTGCGGCGCCGCCGCCGTGCTGGCATTCGAATCGGCGCAGCGCAGCGCCCCCCaaaaaaaaccc > 5:323137/1‑143 (MQ=255)
tgctgAGCGGCGGGGGGGGTGGCATCAAAGTGTTCAAGCTCGCCCGCGATACCGCCTTGCTGACCCCCGCCGGCAGCGCCATCTGCGGCGCCCCCGCCGTGCTGGCATTCCAATCGGCGCGGCGCAGCGCCCCCCATAAAAGCGCCATg < 2:54152/149‑1 (MQ=255)
gggtctgcGGCGTGTGGGGGGGAATTAATGTGTTCACGCCCCCCCGCTATCCCCCGTTGGCCCCCCCCCCCGGCAGCGCCATCGGCGGCGCCGCCCCCGGGCGGCCATCCGACGCGCCGCGGCGCAGCCCCCCCCATAAAAGCGCCATg < 8:73708/142‑1 (MQ=255)
cTGTGGTGTGGCATGAAAGTGTTCAAGCTCGACCGCGATACCGCCTTGCTGACCGCCGCCGGCAGCGCCATCTGCGGCGCCGCCGCCGTGCTGGCATTCGAATCGGCGCTGCGCAGCGCCCCCCCTAAAAGCGCCATGGCAGTCGGCAg > 8:163429/1‑149 (MQ=255)
aaaGTGTTCAAGCTCGACCGCGATACCGCCTTGCTGACCGCCGCCGGCAGCGCCATCTGCGGCGCCGCCGCCGTGCTGGCATTCCAATCGGCGCTGCGCAGCGCCCCCCATAAAAGCGCCATGGCAGTCGGAAGCGTAGTGCTGTTCg < 2:298533/148‑1 (MQ=255)
ggtTCAAGCTCGACCGCGATACCGCCTTGCTGACCGCCGCCGGCAGCGCAATCTGCGGCGCCGCCGCCGTGCTGGAATTCGAATCGGCGCTGCGCAGCGCCCCCCATAAAAGCGCCATGGCAGTCGGAAGCGTAGTGCTGTTCGGTAc < 8:81070/147‑1 (MQ=255)
acgCTCGCCCGCTATACCGCCTTGCTGCCCGCCGCCGGCAGCGCCTTCTGGGGCGCGGCCGCGGTGTTGGATTTCTATTGGGCGCTGCGCAGCGCCCCCCATAAAAGCGCCATGGCAGTCGGAAGCGTAGTGCTGTTCGGTACCTTGt < 2:294415/146‑1 (MQ=255)
cGCCTTGCTGACCGCCGCCGGCAGCGCCATCTGCGGCGCCGCCGCCGTGCTGGCATTCGAATCGGCGCTGCGCACCCCCCCCCCAAAAAGCCCCAAGGCCGTCGGAAGCGGAGTGGGGTTCGGGACCATGTGGATGGTGCGTTAcaca > 6:126653/1‑148 (MQ=255)
gCTGCCCGCCGCCGGCCGCGCCATCTGGGGGGCCGCCGCGGGGCTGGCTTTCGATGCGGCGCGGCGCCGCGCCCCCCATAAAAGCGCCATGGCAGTCGGAAGCGTAGTGCTGTTCGGTACCTTGTCGATGTTCCTTTACCCACTGGCg < 2:15063/148‑1 (MQ=255)
gCTGCCCGCCGCCGGCAGCGCCATCTGCGGCGCCGCCGCGGGGCTGGCATTCGAAGCGGCGCTGCGCCGCCCCCCCCATAAAAGCGCCATGGCAGTCGGAAGCGTAGTGCTGTTCGGTACCTTGTCGATGTTCCTTTACCCACTGGCGa < 1:2126/149‑1 (MQ=255)
ccgccgccgGCTGCGCATTCTGGGGCGCCGCCGCGGTGGTGGCATTCTAATCGGCGCTGCGCAGCGCCCCCCATAAAAGCGCCATGGCAGTCGGAAGCGTAGTGCTGTTCGGTACCTTGTCGATGTTCCTTTACCCACTGGCGATCAAt < 6:96936/149‑1 (MQ=255)
gcccccgGCTGGGCCATCGCCGGCGCCGCCGCGGGGCTGCGAATCGTTCCGCCGCCGCGCTCCCCCCCCCATAAAAGCGCCATGGCAGTCGGAAGCGTAGTGCTGTTCGGTACCTTGTCGATGTTCCTTTACCCACTGGCGATCAATGc < 6:37234/149‑1 (MQ=255)
cgccgGCAGCGCCATCTGCGGCGCCGCCGCCGTGCTGGCATTCGAATCGGCGCTGCGCCGCGCCCCCCATAAAAGCGCCATGGGAGTCGGAAGCGGAGTGCGGGTGGGTTCCTTGTGGGTGTTCCTTTACCCACGGGCGGTGAATGCCg > 2:203545/1‑149 (MQ=255)
gcggccCCGCCGCCGGGCGGGCATTCGACGCGGCGCGGCGCCCCGCCCCCCATAAAAGCGCCATGGCAGTCGGAAGCGTAGTGCTGTTCGGTACCTTGTCGATGTTCCTTTACCCACTGGCGATCAATGCCGGCTGGCTGCATCTGGAt < 7:163429/149‑1 (MQ=255)
cgccgcggTGGTGTAATTCTAAGCGGCGCTGCGCAGCGCCCCCCATAAAAGCGCCATGGCAGTCGGAAGCGTAGTGCTGTTCGGTACCTTGTCGATGTTCCTTTACCCACTGGCGATCAATGCCGGCTGGCTGCATCTGGATACCATgg < 5:117060/149‑1 (MQ=255)
aTTCGAATCGGCGCTGCGCCGCGCCCCCCCAAAAAGCGCCCTGGCAGTCGGAAGCGTTGTGCTGTTCGGTACCGTGTCGATGTTGCTTTACCCACGGGCGCTCAATGCCGGCTGGCGGCATCGGGCTAACATGGGCGCCGGgctgctgc > 4:309806/1‑149 (MQ=255)
aTTCGAATCGGCGCTGCGCAGCGCCCCCCATAAAAGCGCCATGGCAGTCGGAAGCGTAGTGCTGTTCGGTTCCTTGTCGATGTTCCTTTACCCACGGGCGGTCAATGCCGGGGGGCTGGATCTGGGGAGCATGGGCGCCGGgctgctgg > 6:301944/1‑148 (MQ=255)
|
GGTGCTGGTAGTCACCAGTACCCTGCTGATCGGCCTGTGGTGTGGCATGAAAGTGTTCAAGCTCGACCGCGATACCGCCTTGCTGACCGCCGCCGGCAGCGCCATCTGCGGCGCCGCCGCCGTGCTGGCATTCGAATCGGCGCTGCGCAGCGCCCCCCATAAAAGCGCCATGGCAGTCGGAAGCGTAGTGCTGTTCGGTACCTTGTCGATGTTCCTTTACCCACTGGCGATCAATGCCGGCTGGCTGCATCTGGATACCATGGGCGCCGGGCTGCTGC > NC_002947_CJ‑RC/4158323‑4158600
|
| 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
