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 F57 I1 R1
|
57 |
81.4 |
3444058 |
98.4% |
3388953 |
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 | 90.9%
| 21.9
/ ‑5.3
| 11 | 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 (4/6); minor base C (0/1); total (4/7) |
| 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%
| 32.7
/ NA
| 11 | 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 (4/7); total (4/7) |
| * | NC_002947_CJ‑RC | 5,558,423 | 3 | . | C | 100.0%
| 32.7
/ NA
| 11 | 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 (4/7); total (4/7) |
GCTGTCACTGTGCAGGAAATTCAGGTCGGCCTGGGCAGCGATTAGTCGGGCGGACATGAGCAACTCCTTTTGTCATGTGTCGCCGACAGCATAGCAACACCGCTCAGGTGTGGGAGCGGCCTTGTGTCGCGAAAGGGCCGCATAGCG‑‑‑CCGGCAATTTCCGCGTGTATGCAACAAACCTGGGGCTGCTATGCAGCCCTTTCGCGACACAAGGCCCACAAAGGACCGCGCAGGCTTCAGGCCCGGAACTGGCCCAGGCTGGCGCGCAGCTGAGCCGC > NC_002947_CJ‑RC/5558277‑5558551
|||
gCTGTCACTGTGCAGGAAATTCAGGTCGGCCTGGGCAGCGATTAGTCGGGCGGACATGAGCAACTCCTTTTGTCATGTGTCGCCGACAGCATAGCAACACCGCTCAGGTGTGGGAGCGGCCTTGTGTCGCGAAAGGGCCGCATAgcggc < 8:270037/149‑3 (MQ=255)
aaTTCAGGTCGGCCTGGGCAGCGATTAGTCGGGCGGACATGAGCAACTCCTTTTGTCTTGTGTCGCCTACTGCATAGCAACACCGATCAGGTGTGGTAGCGGCCTTGTGTCGCTAAAGGGCCGAATAGCGGCCCCGGCAATTTCcgcg < 2:89375/148‑1 (MQ=255)
tCGGCCTGGGCTGCTATTAGTCGGGCGGACATGAGAAACTCCTTTTGTCATGTGGCGCCGACAGCATAGCACCACCGCTCTGGTGTGGGAGCGGCATTGTGTCGCTAAAGGGCCGAATAGCGGCCCCGGCAATTTCCGCGTGTATGcaa < 2:10850/149‑1 (MQ=255)
gctgCGATTAGTGGGGCGTAAATGAGCAACTCATTTTGTCATGTGTCGCCGAAAGCATAGCAACACCGCTCTGGTGTGGTTGCGGCCTTGTGTCGCTAATGGGCCGAATAGCGGCCCCGGCAATTTCCGCGTGTATGCAACAAACCTgg < 8:184804/146‑1 (MQ=255)
gCAGCGATTAGGCGGGCGTACATGAGAAACTCCTTTTGTCATGTGTCGCCGACAGCATAGAAACCCCGCTCAGGTGTGGGAGCGGCCTTGTGTCGCTAAAGGGCCGCATAGCGGCCCCGGCAATTTCCGCGTGTATGCAACAAACCTgg < 7:135318/149‑1 (MQ=37)
ttgTCGGGCGCACATGAGCAACTCTTTTTGTCATGTGTCGCCGACAGAATAGCAACACCGCTCTGGTGTGGGCGCGGCCTTGTGCCGCTAACGGGCCGAATAGCGGCCCCGGCAATTTCCGCGTGTATGCAACAGACCTGGGgctgct < 4:48462/146‑1 (MQ=255)
cATGAGAAACTCCTTTTGTCTTGTGTCGCCGACAGCATAGCAACCCGGCTCTGGTGTGGGCGCGGCGTTGGGGCGCTAATGGGCCGCATAGCGGCCCCGGCAATTTCCGCGTGTATGCAACAAACCTGGGGCTGCTATGCAGCCCttt < 4:50408/148‑1 (MQ=255)
aTAGCAACACCGCTCAGGTGTGGGAGCGGCCTTGTGTCGCGAAAGGGCCGCATAGCGGCCCCGGCAATTTACGCGTGTATGcaa > 1:180226/1‑84 (MQ=18)
tAGCAACCCCGCTCTGGTGTGGGAGGGGCGTTGTGTCGCTAACGGGCCGATTAGCGCCCCCGGCAATTTCCGCGTGTATGCAACAAACCTGGGGCTGCTATGCAGCCCTTTCGCGACACATGGCCCACAAAGGACCGCGCAGGCTTCAg < 7:222690/149‑1 (MQ=255)
ttGTGTCGCGAAAGGGCCGCTTAGCGGCCCCGGGAATTTCCGCGTGTATGCACCAAACCTGGGGCTGCTATGCAGCCCTTTCGCGACACAAGGCCCACAAAGGACCGCGCAGGCTTCCGGCCCGGAACTGGCCCAGGCTGGCGcgccgc > 5:303550/1‑149 (MQ=37)
gAAAGGGCCGCATAGCGGCCCCGGCAATTTCCGCGTGTATGCAACAAACCTGGGGCTGCTATGCAGCCCTTTCGCGACACAAGGCCCACAAAGGACCGCGCAGGCTTCAGGCCCGGAACTGGCCCAGGCTGGCGCGCAGCTGAgccgc > 2:365389/1‑148 (MQ=255)
gAAAGGGCCGCATAGCGGCCCCGGCAATTTCCGCGTGTATGCAACAAACCTGGGGCTGCTATGCAGCCCTTTCGCGACACAAGGCCCACAAAGGACCGCGCAGGCTTCAGGCCCGGAACTGGCCCAGGCTGGCGCGCAGCTGAgccgc > 3:75390/1‑148 (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
