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 F22 I1 R1
|
55 |
83.2 |
3548070 |
98.1% |
3480656 |
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 | 86.7%
| 36.8
/ ‑4.5
| 16 | intergenic (‑84/+87) | PP_4887/PP_4888 | hypothetical protein/methyl‑accepting chemotaxis transducer |
| Reads supporting (aligned to +/- strand): ref base . (0/1); major base G (7/6); minor base C (0/2); total (7/9) |
| Fisher's exact test for biased strand distribution p-value = 4.67e-01 |
| Kolmogorov-Smirnov test that lower quality scores support variant p-value = 1.00e+00 |
| * | NC_002947_CJ‑RC | 5,558,423 | 2 | . | C | 93.8%
| 49.2
/ ‑2.7
| 16 | intergenic (‑84/+87) | PP_4887/PP_4888 | hypothetical protein/methyl‑accepting chemotaxis transducer |
| Reads supporting (aligned to +/- strand): ref base . (0/1); new base C (7/8); total (7/9) |
| 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 | 3 | . | C | 87.5%
| 46.0
/ 0.9
| 16 | 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 (7/7); total (7/9) |
| Fisher's exact test for biased strand distribution p-value = 4.75e-01 |
| Kolmogorov-Smirnov test that lower quality scores support variant p-value = 1.00e+00 |
TCACTGTGCAGGAAATTCAGGTCGGCCTGGGCAGCGATTAGTCGGGCGGACATGAGCAACTCCTTTTGTCATGTGTCGCCGACAGCATAGCAACACCGCTCAGGTGTGGGAGCGGCCTTGTGTCGCGAAAGGGCCGCATA‑‑‑GCG‑‑‑CC‑GGCAATTTCCGCGTGTATGCAACAAACCTGGGGCTGCTATGCAGCCCTTTCGCGACACAAGGCCCACAAAGGACCGCGCAGGCTTCAGGCCCGGAACTGGCCCAGGCTGGCGCGCAGCTGAGCCGC > NC_002947_CJ‑RC/5558281‑5558551
|||
tCACTGTGCAGGAAATTCAGGTCGGCCTGGGCAGCGATTAGTCGGGCGGACATGAGCAACTCCTTTTGTCATGTGTCGCCGACAGCATAGCAACACCGCTCAGGTGTGGGAGCGGCCTTGTGTCGCGAAAGGGCCGCATA‑‑‑gcggccc < 6:19395/147‑5 (MQ=255)
tCACTGTGCAGGAAATTCAGGTCGGCCTGGGCAGCGATTAGTCGGGCGGACATGAGCAACTCCTTTTGTCATGTGTCGCCGACAGCATAGCAACACCACTCAGGTGTGGGAGCGGCCTTGTGTCGCGAAAGGGCCGCATA‑‑‑gcggccccg < 5:336739/149‑7 (MQ=255)
aGGAAATTCTGGGCGGCCTGGGCAGCGATTAGGGGGGCGCACATTAGCAACTCCTTTTGTCATGTGTCGCCGACAGAATAGCAACCCCGCTCTGGTGTGGGAGCGGCCTTGTGTCGCTAATGGGCCGCATC‑‑‑GCGGCCCC‑GGCAATTTcc < 2:115831/149‑1 (MQ=25)
gggcGGCCTGGCCCGCTATTAGGCGGGCGCAAATTAGAAACTCTTTTTGTCATGTGGCCCCTAATGAATACAAACCCCGCTCTGGTGGGGGAGCGGCCTTGTGTCGCTAACGGCCCCAATA‑‑‑GCGCCCCC‑GGCAATTTCCGCGTGTATGc < 2:193882/146‑1 (MQ=255)
ttAGTCGGGCGGAAATGAGCAACTCCTTTTGTCATGGGTCGCCGACAGCATAGCAACACCGCTCAGGTGTGGGAGCGGCCTTGTGTCGCTAAAGGGCCGCATA‑‑‑GCGGCCCC‑GGCAATTTCCGCGTGTATGCAACAAACCTGGGgctgc < 2:37076/148‑1 (MQ=38)
gTCGGGCGGACATGAGCAACTCCTTTTGTCATGTGTCGCCGACAGCATAGCAACACCGCTCAGGTGTGGGAGCGGCCTTGTGTCGCGAAAGGGCCGCATA‑‑‑GCGGCCCC‑GGCAATTTCCGCGTGTATGCAACAAACCTGGGGCTGCTATg > 3:185299/1‑149 (MQ=255)
cGGGCGCACATGCGCAACCCCTTTTGTCATGTGTCCCCTACACCAAACCAACCCCGCTCCGGTGTGGGCGCGGCCTTGTGGCGCGAACGGCCCGAATA‑‑‑GCGGCCCC‑GGCAATTTCCGCGTGTATGCAACAAACCTGGGGCTGCTATGCa < 6:355991/149‑1 (MQ=255)
taCATGAGCAACTCGTTTTGTCATGTGTCGCCGACAGAATACAAACACGGCTCTGGGGTGGGTGCGGCTTTGTGGCGCTAAAGGGCCTAATA‑‑‑GCGCCCCC‑GGCAATTTCCGCGTGTATGCAACAAACCTGGGGCTGCTATGCAGCCCtt < 1:282556/148‑1 (MQ=255)
gcgCAACTCCTTTTGTCTGGTGTCGCCGACAGCATAGCAACACCGCTCTGGTGTGGGTGGGGCTTTGTGTCGCGAACGGGCCGCATA‑‑‑GCGGCCCC‑GGCAATTTCCGCGTGTATGCAACAAACCTGGGGCTGCTATGCAGCCCTTTcgc < 4:185299/146‑1 (MQ=255)
gAGCAACTGATTTTGTATTTTTTCGCCTACAGATTTGAAACACCGCGCTGGTGTGGTCGGGGCTTTGTGGCGCTAATGGGCGGCTTAGGGGCC‑‑‑CC‑GGCAATTTCCGCGTGTATGCAACAAACCTGGGGCTGCTATGCAGCCCTTTcgc < 8:395305/148‑1 (MQ=255)
gtgtCGCCGACAGCATAGCAACACCGCTCAGGTGTGGGAGCGGCCTTGTGTCGCGAAAGGGCCGCATA‑‑‑GCGGCCCC‑GGCAATTTCCGCGTGTATGCAACAAACCTGGGGCTGCTATGCAGCCCTTTcgc > 3:410904/1‑129 (MQ=37)
gtgtCGCCGACAGCATAGCAACACCGCTCAGGTGTGGGAGCGGCCTTGTGTCGCGAAAGGGCCGCATA‑‑‑GCGGCCCC‑GGCAATTTCCGCGTGTATGCAACAAACCTGGGGCTGCTATGCAGCCCTTTcgc < 4:410904/129‑1 (MQ=37)
tggTGTGGGAGCGGCTTTGTGGCCCTAACGGGCCGCTTC‑‑‑GCGGC‑CCGGGCAATTTCCGCGTGTATCCAACAAACCTGGGGCTGCTATGCAGCCCTTTCGCGACACAAGGCCCACAAAGGACCGCGCAGGCTTCAGGCCCGGAACTgg < 8:4209/146‑1 (MQ=255)
tCGCGAAAGGGCCGCATA‑‑‑GCGGCCCC‑GGCAATTTCCGCGTGTATGCAACAAACCTGGGGCTGCTATGCAGCCCTTTCGCGACACAAGGCCCACAAAGGACCGCGCAGGCTTCAGGCCCGGAACTGGCCCAGGCTGGCGCGCAGCTGAgc > 4:227744/1‑149 (MQ=255)
tCGCGAAAGGGCCGCATA‑‑‑GCGGCCCC‑GGCAATTTCCGCGTGTATGCAACAAACCTGGGGCTGCTATGCAGCCCTTTCGCGACACAAGGCCCACAAAGGACCGCGCAGGCTTCAGGCCCGGAACTGGCCCAGGCTGGCGCGCAGCTGAgc > 1:92890/1‑149 (MQ=255)
gcgAAAGGGCCGCATA‑‑‑GCGGCCCC‑GGCAATTTCCGCGTGTATGCAACAAACCTGGGGCTGCTATGCAGCCCTTTCGCGACACAAGGCCCACAAAGGACCGCGCAGGCTTCAGGCCCGGAACTGGCCCAGGCTGGCGCGCAGCTGAgccg > 3:380848/1‑149 (MQ=255)
cgAAAGGGCCGCATA‑‑‑GCGGCCCC‑GGCAATTTCCGCGTGTATGCAACAAACCTGGGGCTGCTATGCAGCCCTTTCGCGACACAAGGCCCACAAAGGACCGCGCAGGCTTCAGGCCCGGAACTGGCCCAGGCTGGCGCGCAGCTGAgccgc > 2:17920/1‑149 (MQ=255)
aaGGGCCGCATA‑‑‑GCGGCCCC‑GGCAATTTCCGCGTGTATGCAACAAACCTGGGGCTGCTATGCAGCCCTTTCGCGACACAAGGCCCACAAAGGACCGCGCAGGCTTCAGGCCCGGAACTGGCCCAGGCTGGCGCGCAGCTGAgccgc > 8:364237/1‑146 (MQ=255)
|||
TCACTGTGCAGGAAATTCAGGTCGGCCTGGGCAGCGATTAGTCGGGCGGACATGAGCAACTCCTTTTGTCATGTGTCGCCGACAGCATAGCAACACCGCTCAGGTGTGGGAGCGGCCTTGTGTCGCGAAAGGGCCGCATA‑‑‑GCG‑‑‑CC‑GGCAATTTCCGCGTGTATGCAACAAACCTGGGGCTGCTATGCAGCCCTTTCGCGACACAAGGCCCACAAAGGACCGCGCAGGCTTCAGGCCCGGAACTGGCCCAGGCTGGCGCGCAGCTGAGCCGC > NC_002947_CJ‑RC/5558281‑5558551
|
| 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
