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 |
|
A4 F58 I1 R1
|
60 |
66.0 |
2910360 |
98.3% |
2860883 |
145.7 |
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 | 83.3%
| 20.2
/ ‑4.3
| 14 | intergenic (‑84/+87) | PP_4887/PP_4888 | hypothetical protein/methyl‑accepting chemotaxis transducer |
| Reads supporting (aligned to +/- strand): ref base . (0/2); major base G (3/7); minor base C (0/2); total (3/11) |
| 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 | 85.7%
| 37.4
/ 1.0
| 14 | intergenic (‑84/+87) | PP_4887/PP_4888 | hypothetical protein/methyl‑accepting chemotaxis transducer |
| Reads supporting (aligned to +/- strand): ref base . (0/2); new base C (3/9); total (3/11) |
| 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 | 3 | . | C | 85.7%
| 36.9
/ 1.0
| 14 | intergenic (‑84/+87) | PP_4887/PP_4888 | hypothetical protein/methyl‑accepting chemotaxis transducer |
| Reads supporting (aligned to +/- strand): ref base . (0/2); new base C (3/9); total (3/11) |
| Fisher's exact test for biased strand distribution p-value = 1.00e+00 |
| Kolmogorov-Smirnov test that lower quality scores support variant p-value = 9.76e-01 |
ACTGTGCAGGAAATTCAGGTCGGCCTGGGCAGCGATTAGTCGGGCGGACATGAGCAACTCCTTTTGTCATGTGTCGCCGACAGCATAGCAACACCGCTCAGGTGTGGGAGCGGCCTTGTGTCGCGAAAGGGCCGCATA‑‑‑G‑‑‑CG‑‑‑CCGGCAATTTCCGCGTGTATGCAACAAACCTGGGGCTGCTATGCAGCCCTTTCGCGACACAAGGCCCACAAAGGACCGCGCAGGCTTCAGGCCCGGAACTGGCCCAGGCTGGCGCGCAGCTGAGCCGC > NC_002947_CJ‑RC/5558283‑5558551
|||
aCTGTGCAGGAAATTCAGGTCGGCCTGGGCAGCGATTAGTCGGGCGGACATGAGCAACTCCTTTTGTCATGTGTCGCCGACAGCATAGCAACACCGCTCAGGTGTGGGAGCGGCCTTGTGTCGCTAAAGGGCCGCATA‑‑‑g‑‑‑cggccccgg < 7:332287/148‑8 (MQ=255)
ggggCCTGGGCTGCTTTTTGTCGGGGGGACATGCGCAAATCCTTTTTTCTTGTGGCGCCGACTGCATATCAACAGCGCGCCGGGGTGGTCGCGGCGTGGTGTCGCTAAGGGGCCGCTTAGGGG‑‑‑CC‑‑‑CCGGCAATTTCCGCGTGTATGcaa < 8:322957/147‑1 (MQ=255)
ccTGGGCAGCGATTAGTCGGGCGGACATGAGCAACTCCTTTTGTATTGTGTCGCCGACTGCATAGCAACACCGCTCAGGTGTGGGAGCGGCCTTGTGTCGCTAATGGGCCGCATA‑‑‑G‑‑‑CGGCCCCGGCAATTTCCGCGTGTATGcaacaa < 6:286442/148‑1 (MQ=37)
cTGGGCAGCGATTAGTCGGGCGGACATGAGCAACTCCTTTTGTCATGTGTCGCCGACAGCATAGCAACACCGCTCAGGTGTGGGAGCGGCCTTGTGTCGCTAAAGGGCCGCATA‑‑‑G‑‑‑CGGCCCCGGCAATTTCCGCGTGTATGCAACaaa < 2:35867/148‑1 (MQ=38)
gCAGCTTTTAGTCGGGCGCAAATGAGAAACTCGTTTTGTCTTGTGGCGCCGACAGCATAGCAACCCCGCTCTGGTGTGGGAGGGGCCTTGTGTCGCGAACGGCCCGCATA‑‑‑G‑‑‑CGGCCCCGGCAATTTCCGCGTGTATGCAACAAACCTg < 6:273365/148‑1 (MQ=255)
ctgCGATTAGTGGGGCGGACATTACAAACTCTTTTTGTCTTGTGTCGCCGACAGCATAGAACCCCCCCTCTGGTGGGGGTGCGGCCTTGTGTCGCTAACGGGCCGCTTA‑‑‑G‑‑‑CGGCCCCGGCAATTTCCGCGTGTATGCAACAAACCTgg < 4:232164/146‑1 (MQ=255)
aGCGATTAGTCGGGCGGACATGAGCAACTCCTTTTGTCATGTGTCGCCTACAGCATAGCAACACCGCTCAGGTGTGGGAGCGGCCTTGTGTCGCGAAAGGGCCGCATA‑‑‑G‑‑‑CGGCCCCGGCAATTTCCGCGTGTATGCAACAAACCTgggg < 8:285880/149‑1 (MQ=38)
taccaccTCCTTTTGTTTTGGGCCGCCGACAGCATAGCAACCCCGCTCCGGTGTGGGTGGGGCGTTGTGTCGCTAATGGGCCGAATT‑‑‑GGGCCC‑‑‑CCGGCAATTTCCGCGTGTATGCAACAAACCTGGGGCTGCTATGCAGCCCTTTcg < 4:204293/141‑1 (MQ=255)
cAACTCTTTTTGTCTTGTGGCGCCGACAGCATAGCAACACCGCTCTGGTGTGGGAGCGGCCTTGTGTCGCTAATGGGCCGAATA‑‑‑G‑‑‑CGGCCCCGGCAATTTCCGCGTGTATGc < 7:321790/112‑1 (MQ=21)
cAACTCCTTTTGTCATGTGTCGCCGACAGCATAGCAACACCGCTCAGGTGTGGGAGCGGCCTTGTGTCGCGAAAGGGCCGCATA‑‑‑G‑‑‑CGGCCCCGGCAATTTCCGCGTGTATGc > 8:321790/1‑112 (MQ=37)
aaCTCTTTTTGTCTTGTGCCGCCGACTGAATACCAACACCGCTCCGGGGGGGGCGCGGCGTGGGGGCGCGATTGGCCCGCTTA‑‑‑G‑‑‑CGCCCCCGGCAATTTCCGCGTGTATGCAACAAACCTGGGGCTGCTATGCAGCCCTTTCGCGaca < 4:127509/148‑1 (MQ=255)
atcccAACCCCGCTCCGGTGGGGGCGCGGCCTTGTGCCCCTAACGGCCCCCATC‑‑‑G‑‑‑CGCCCCCGGCAATTGCCGCGTGTATCCAACAAACCTGGGGCTGCTATGCAGCCCTTGCGCGACACAAGGCCCACAAAGGACCGCGCAGGCTTCa < 8:1498/145‑1 (MQ=255)
tgGGAGCGGCCTTGTGTCGCTAACGGGCCTCATA‑‑‑G‑‑‑CGGCCCCGGCAATTTCCGCGTGTATGCAACAAACCTGGGGCTGCTATGCAGCCCTTTCGCGACACAAGGCCCACAAAGGACCGCGCAGGCTTCAGGCCCGGAACTGGCCCAg < 6:274035/147‑1 (MQ=37)
gtgtCGCGAAAGGGCCGCATA‑‑‑G‑‑‑CGGCCCCGGCAATTTCCGCGTGTATGCAACAAACCTGGGGCTGCTATGCAGCCCTTTCGCGACACAAGGCCCACAAAGGACCGCGCAGGCTTCAGGCCCGGAACTGGCCCAGGCTGGCGCGCAGCt > 8:871/1‑148 (MQ=255)
ggCCGCATA‑‑‑G‑‑‑CGGCCCCGGCAATTTCCGCGTGTATGCAACAAACCTGGGGCTGCTATGCAGCCCTTTCGCGACACAAGGCCCACAAAGGACCGCGCAGGCTTCAGGCCCGGAACTGGCCCAGGCTGGCGCGCAGCTGAgccgc > 6:128961/1‑143 (MQ=255)
|||
ACTGTGCAGGAAATTCAGGTCGGCCTGGGCAGCGATTAGTCGGGCGGACATGAGCAACTCCTTTTGTCATGTGTCGCCGACAGCATAGCAACACCGCTCAGGTGTGGGAGCGGCCTTGTGTCGCGAAAGGGCCGCATA‑‑‑G‑‑‑CG‑‑‑CCGGCAATTTCCGCGTGTATGCAACAAACCTGGGGCTGCTATGCAGCCCTTTCGCGACACAAGGCCCACAAAGGACCGCGCAGGCTTCAGGCCCGGAACTGGCCCAGGCTGGCGCGCAGCTGAGCCGC > NC_002947_CJ‑RC/5558283‑5558551
|
| Alignment Legend |
|---|
Aligned base mismatch/match (shaded by quality score): ATCG/ATCG < 3 ≤ ATCG/ATCG < 14 ≤ ATCG/ATCG < 15 ≤ ATCG/ATCG < 16 ≤ ATCG/ATCG < 36 ≤ ATCG/ATCG |
Unaligned base: atcg Masked matching base: atcg Alignment gap: ‑ Deleted base: ‑ |
GATK/CNVnator alignment
N/A
