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 F58 I1 R1
|
57 |
79.2 |
3360594 |
98.6% |
3313545 |
146.6 |
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 | 92.9%
| 32.6
/ ‑6.0
| 14 | intergenic (‑84/+87) | PP_4887/PP_4888 | hypothetical protein/methyl‑accepting chemotaxis transducer |
| Reads supporting (aligned to +/- strand): ref base . (0/0); major base G (5/8); minor base C (0/1); total (5/9) |
| 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 |
| * | NC_002947_CJ‑RC | 5,558,423 | 2 | . | C | 100.0%
| 43.2
/ NA
| 14 | 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 (5/9); total (5/9) |
| * | NC_002947_CJ‑RC | 5,558,423 | 3 | . | C | 100.0%
| 44.4
/ NA
| 14 | 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 (5/9); total (5/9) |
GCTGTCACTGTGCAGGAAATTCAGGTCGGCCTGGGCAGCGATTAGTCGGGCGGACATGAGCAACTCCTTTTGTCATGTGTCGCCGACAGCATAGCAACACCGCTCAGGTGTGGGAGCGGCCTTGTGTCGCGAAAGGGCCGCATAGCG‑‑‑CCGGCAATTTCCGCGTGTATGCAACAAACCTGGGGCTGCTATGCAGCCCTTTCGCGACACAAGGCCCACAAAGGACCGCGCAGGCTTCAGGCCCGGAACTGGCCCAGGCTGGCGCGCAGCTGAGCCGC > NC_002947_CJ‑RC/5558277‑5558551
|||
gCTGTCACTGTGCAGGAAATTCAGGTCGGCCTGGGCAGCGATTAGTCGGGCGGACATGAGCAACTCCTTTTGTCATGTGTCGCCGACAGCATAGCAACACCGCTCAGGTGTGGGAGCGGCCTTGTGTCGCGAAAGGGCCGCATAgcg < 7:94296/147‑1 (MQ=255)
tCAGGTCGGCCTGGGCAGCGATTAGTCGGGCGGACATGAGCAACTCCTTTTGTCATGTGTCGCCGACAGCATAGCAACACCGCTCAGGTGTGGGAGCGGCCTTGTGTCGCGAAAGGGCCGCATAGCGGCCCCGGCAATTTCCGCGTGTa > 5:64580/1‑149 (MQ=255)
cAGGTCGGCCTGGGCAGCGATTAGGCGGGCGGACATGAGCAACTCCTTTTGTCATGTGACGCCTACAGCATAGCAACACCGCTCTGGTGTGGGAGCGGCCTTGTGGCGCTAAAGGGCCGCATAGCGGCCCCGGCAATTTCCGCGTGTa < 2:88658/148‑1 (MQ=255)
ggggggttGGGCTGCTATTTGTGGGGCTTACTTTTGCAACTTTTTTTGTTATGTGTCTCCTACATCTTATAAACCCCTCTCTGGTGTGGGAGGGGCTTTGTGGCGCTAAAGGGCCGCATTGCGCCCCCGGCAATTTCCGCGTGTATGc < 4:398506/141‑1 (MQ=255)
tttggcGGGCGTACATGTGCAACTCTTTTTGTCTTGGGTCGCCGACTTCAATGCAACACCGCTCAGGGGTGGTAGCGGCTTTGGGGCGCTAATGGCCGGCATTGCGGCCCCGGCAATTTCCGCGTGTATGCAACAAACCTGGGgctgct < 6:375777/144‑1 (MQ=255)
ggcGGGCGTAAATGACCAACTCCTTTTGTCTTGTGCCCCCGACAGCATAGCAACCCCGCTCCGGTGTGGGTGCGGCCTTGTGGCGCTAACGGGCCGAATCGCGGCCCCGGCAATTTCCGCGTGTATGCAACAAACCTGGGGCTGCTAt < 6:237211/146‑1 (MQ=255)
tCGGGCGGACATGAGCATCTCCTTTTTTCATGTGTCGCCGACTGAATAGCAACACCGCTCAGGTTTGGGAGCGGCCTTGTGTCGCTAAAGGGCCGCATAGCGGCCCCGGCAATTTCCGCGTGTATGCAACAAACCTGGGGCTGCTATg < 2:268018/148‑1 (MQ=37)
gggCGTACATGAGCAACTCCTTTTGTCATGTGTCGCCTACAGAATAGCAACACCGCTCTGGTGTGGGAGCGGCCTTGTGTCGCTAACGGGCCGAATAGCGGCCCCGGCAATTTCCGCGTGTATGCAACAAACCTGGGGCTGCTATGCAg < 6:64580/149‑1 (MQ=37)
tGAGCAACTCATTTTGTCTTGTGCCCCCGACAGAATAGCAACACCCCTCTGGTGTGGGCGCGGCCTTGTGGCGCTAACGGGCCGCATCGCGGCCCCGGCAATTTCCGCGTGTATGCAACAAACCTGGGGCTGCTATGCAGCCCTTTcgc < 6:24777/149‑1 (MQ=255)
aGCAACTCCTTTTGTCATGTGGCGCCGACAGCATAGCAACACCGCTCAGGTGTGGGAGCGGCCTTGTGTCGCTAAAGGGCCGCATAGCGGCCCCGGCAATTTCCGCGTGTATGCAACAAACCTGGGGCTGCTATGCAGCCCTTTcgcg < 2:1328/148‑1 (MQ=38)
acacGGCTCTGTTGGGGGAGGGGCGTTGGGTCGCTAACGGCCCGAATCGCGGCCCCGGCAATTTCCGCGTGTATCAAACAAACCTGGGGCTGCTATGCAGCCCTTTCGCTACACAAGGCCCACAAAGGACCGCGCAGGCTTCAGGCCCg < 6:114690/149‑1 (MQ=255)
ttGTGTCGCGAAAGGGCCGCATAGCGGCCCCGGCAATTTCCGCGTGTATGCAACAAACCTGGGGCTGCTATGCAGCCCTTTCGCGACACAAGGCCCACAAAGGACCGCGCAGGCTTCAGGCCCGGAACTGGCCCAGGCTGGCGCGCAGc > 6:397322/1‑149 (MQ=255)
tCGCGAAAGGGCCGCATAGCGGCCCCGGCAATTTCCGCGTGTATGCAACAAACCTGGGGCTGCTATGCAGCCCTTTCGCGACACAAGGCCCACAAAGGACCGCGCAGGCTTCAGGCCCGGAACTGGCCCAGGCTGGCGCGCAGCTGAg > 7:83787/1‑148 (MQ=255)
cgAAAGGGCCGCATAGCGGCCCCGGCAATTTCCGCGTGTATGCAACAAACCTGGGGCTGCTATGCAGCCCTTTCGCGACACAAGGCCCACAAAGGACCGCGCAGGCTTCAGGCCCGGAACTGGCCCAGGCTGGCGCGCAGCTGAgccg > 7:197421/1‑148 (MQ=255)
aGGGCCGCATAGCGGCCCCGGCAATTTCCGCGTGTATGCAACAAACCTGGGGCTGCTATGCAGCCCTTTCGCGACACAAGGCCCACAAAGGACCGCGCAGGCTTCAGGCCCGGAACTGGCCCAGGCTGGCGCGCAGCTGAgccgc > 4:170612/1‑145 (MQ=255)
|||
GCTGTCACTGTGCAGGAAATTCAGGTCGGCCTGGGCAGCGATTAGTCGGGCGGACATGAGCAACTCCTTTTGTCATGTGTCGCCGACAGCATAGCAACACCGCTCAGGTGTGGGAGCGGCCTTGTGTCGCGAAAGGGCCGCATAGCG‑‑‑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
