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 |
|
A2 F18 I1 R1
|
58 |
60.4 |
2754136 |
98.2% |
2704561 |
146.5 |
Breseq alignment
BRESEQ :: Evidence
|
| evidence |
seq id |
position |
mutation |
annotation |
gene |
description |
| RA |
NC_002947_CJ‑RC |
5,558,423 |
+GCC |
intergenic (‑84/+87) |
PP_4887 ← / ← PP_4888 |
hypothetical protein/methyl‑accepting chemotaxis transducer |
|
| |
seq id |
position |
ref |
new |
freq |
score (cons/poly) |
reads |
annotation |
genes |
product |
| * | NC_002947_CJ‑RC | 5,558,423 | 1 | . | G | 100.0%
| 31.1
/ NA
| 12 | intergenic (‑84/+87) | PP_4887/PP_4888 | hypothetical protein/methyl‑accepting chemotaxis transducer |
| Reads supporting (aligned to +/- strand): ref base . (0/0); new base G (5/7); total (5/7) |
| * | NC_002947_CJ‑RC | 5,558,423 | 2 | . | C | 100.0%
| 34.9
/ NA
| 12 | intergenic (‑84/+87) | PP_4887/PP_4888 | hypothetical protein/methyl‑accepting chemotaxis transducer |
| Reads supporting (aligned to +/- strand): ref base . (0/0); new base C (5/7); total (5/7) |
| * | NC_002947_CJ‑RC | 5,558,423 | 3 | . | C | 100.0%
| 35.5
/ NA
| 12 | intergenic (‑84/+87) | PP_4887/PP_4888 | hypothetical protein/methyl‑accepting chemotaxis transducer |
| Reads supporting (aligned to +/- strand): ref base . (0/0); new base C (5/7); total (5/7) |
GCTGTCACTGTGCAGGAAATTCAGGTCGGCCTGGGCAGCGATTAGTCGGGCGGACATGAGCAACTCCTTTTGTCATGTGTCGCCGACAGCATA‑GCAACACCGCTCAGGTGTGGGAGCGGCCTTGTGTCGCGAAAGGGCCGCATAGCG‑‑‑CCGGCAATTTCCGCGTGTATGCAACAAACCTGGGGCTGCTATGCAGCCCTTTCGCGACACAAGGCCCACAAAGGACCGCGCAGGCTTCAGGCCCGGAACTGGCCCAGGCTGGCGCGCAGCTGAGCCGC > NC_002947_CJ‑RC/5558277‑5558551
|||
gCTGTCACTGTGCAGGAAATTCAGGTCGGCCTGGGCAGCGATTAGTCGGGCGGACATGAGCAACTCCTTTTGTCATGTGTCGCCGACAGCATA‑GCAACACCGCTCAGGTGTGGGAGCGGCCTTGTGTCGCGAAAGGGCCGCATAgcggc < 6:143721/149‑3 (MQ=255)
ggAAATTCAGGTCGGCCTGGGCAGCGATTAGTCGGGCGGACATGAGCAACTCCTTTTGTCATGTGTCGCCGACAGCATA‑GCAACACCGCTCAGGTGTGGGAGCGGCCTTGTGTCGCGAAAGGGCCGCATAGCGGCCCCGGCAATTTCcg > 6:247436/1‑149 (MQ=255)
ctggggggCCTGGGCTGCTATTTGTCGGGCGCACATGTCAAACTCTTTTTTTCTTGTGGCGCCGACAG‑ATATGCAACCCCGCGGCGGTGTGGGCGCGGCGTTGTGGGGCTAAGGGGCCGAATAGCGGCCCCGGCAATTTCCGCGTGTa < 8:134257/142‑1 (MQ=255)
ccggTCGGCCGGGGCAGCTATTAGTCGGGCGTACATGAGCAACTCCTTTTGTCTTGTGTCCCCTACAGAATC‑GCAACCCCGCTCAGGTGTGGGAGCGGCGTTGTGCCGCTAATGGGCCGCATTGCGGCCCCGGCAATTTCCGCGTGTAt < 2:78195/147‑1 (MQ=255)
ggTCGGCGTGGGCAGCGATTAGTCGGGCGTACATGAGCAACTCCTTTTGTCTTGTGCCGCCGACAGCATA‑CCAACACCGCTCTGGTGTGGGCGCGGCGTTGTGTCGCTAAAGGGCCGAATAGCGGCCCCGGCAATTTCCGCGTGTATGc < 6:296326/149‑1 (MQ=255)
cTGGGCAGCTATTAGTCGGGCGGACATGAGCAACTCCTTTTGTCATGTGTCGCCGACAGCATA‑GCAACACCGCTCAGGTGTGGGAGCGGCCTTGTGGCGCTAAAGGGCCGAATAGCGGCCCCGGCAATTTCCGCGTGTATGCAACAAAc < 7:186177/149‑1 (MQ=255)
tCGGGCGGACATGAGCAACTCCTTTTGTCATGTGTCGCCGACAGCATA‑GCAACACCGCTCAGGTGTGGGAGGGGCCTTGTGTCGCGAAAGGGCCGCATAGCGGCCCCGGCAATTTCCGCGTGTATGCAACAAACCTGGGGCTGCTATGc < 8:344706/149‑1 (MQ=38)
aCATGAGCAACTCCTTTTGTCTTGTGTCGCCGACAGCATA‑CCAACACCGCTCTGGTGTGGGAGGGGCCTTGTGGCGCTAACGGGCCGCATAGCGGCCCCGGCAATTTCCGCGTGTATGCAACAAACCTGGGGCTGCATAGCAGccccag < 5:247436/149‑4 (MQ=255)
tgGGAGCGGCCTTGTGTCGCGAAAGGGCCGCATAGCGGCCCCGGCAATTTCCGCGTGTATGCAACAAACCTGGGGCTGCTAt > 7:339508/1‑82 (MQ=18)
tgGGAGCGGCCTTGTGTCGCGAAAGGGCCGCATAGCGGCCCCGGCAATTTCCGCGTGTATGCAACAAACCTGGGGCTGCTAt < 8:339508/82‑1 (MQ=18)
tgtgTCGCGAAAGGGCCGCATAGCGGCCCCGGCAATTTCCGCGTGTATGCAACAAACCTGGGGCTGCTATGCAGCCCTTTCGCGACACAAGGCCCACAAAGGACCGCGCAGGCTTCAGGCCCGGAACTGGCCCAGGCTGGCGCGCAGCt > 2:100818/1‑149 (MQ=255)
gcgAAAGGGCCGCATAGCGGCCCCGGCAATTTCCGCGTGTATGCAACAAACCTGGGGCTGCTATGCAGCCCTTTCGCGACACAAGGCCCACAAAGGACCGCGCAGGCTTCAGGCCCGGAACTGGCCCAGGCTGGCGCGCAGCTGAgccg > 4:311244/1‑149 (MQ=255)
cgAAAGGGCCGCATAGCGGCCCCGGCAATTTCCGCGTGTATGCAACAAACCTGGGGCTGCTATGCAGCCCTTTCGCGACACAAGGCCCACAAAGGACCGCGCAGGCTTCAGGCCCGGAACTGGCCCAGGCTGGCGCGCAGCTGAgccgc > 7:75738/1‑149 (MQ=255)
|||
GCTGTCACTGTGCAGGAAATTCAGGTCGGCCTGGGCAGCGATTAGTCGGGCGGACATGAGCAACTCCTTTTGTCATGTGTCGCCGACAGCATA‑GCAACACCGCTCAGGTGTGGGAGCGGCCTTGTGTCGCGAAAGGGCCGCATAGCG‑‑‑CCGGCAATTTCCGCGTGTATGCAACAAACCTGGGGCTGCTATGCAGCCCTTTCGCGACACAAGGCCCACAAAGGACCGCGCAGGCTTCAGGCCCGGAACTGGCCCAGGCTGGCGCGCAGCTGAGCCGC > NC_002947_CJ‑RC/5558277‑5558551
|
| 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
