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 |
|
A3 F14 I0 R1
|
206 |
76.7 |
3255580 |
98.8% |
3216513 |
146.3 |
Breseq alignment
BRESEQ :: Evidence
|
| evidence |
seq id |
position |
mutation |
freq |
annotation |
gene |
description |
| RA |
NC_002947_CJ‑RC |
3,323,603 |
T→G |
23.4% |
D97A (GAC→GCC) |
PP_2923 ← |
hypothetical protein |
|
| |
seq id |
position |
ref |
new |
freq |
score (cons/poly) |
reads |
annotation |
genes |
product |
| * | NC_002947_CJ‑RC | 3,323,603 | 0 | T | G | 23.4%
| 19.3
/ 2.1
| 28 | D97A (GAC→GCC) | PP_2923 | hypothetical protein |
| Reads supporting (aligned to +/- strand): ref base T (9/11); new base G (3/3); total (12/16) |
| Fisher's exact test for biased strand distribution p-value = 1.00e+00 |
| Kolmogorov-Smirnov test that lower quality scores support variant p-value = 8.82e-01 |
CTGCAAGTGCTCAGCCAGTTCCTCTGGCAACGGCACGAAGCGTACAAACGCGTGCAAGTGATGCGCCTCGCGGGTTACCTGCTTGATGCGCCGTTGCAGCTCACTGCCCAGCCGGTCACCGGCCAGCATTGCC‑GTGCGGTCGCCATGGGCGACGCGCCACAGCACTTCATACAGCAGGTTCCAGCGCTGCTCGCCACGGTAGCGAGAGGCCTGCTCCAACTGGCTCAGCAGTGCGGCCGGGAC‑TTTGGCCCGGAAAGGGCCCGGCCCGTCAGGCGGCGCTGCCGGCA > NC_002947_CJ‑RC/3323464‑3323750
|
cTGCAAGTGCTCAGCCAGTTCCTCTGGCAACGGCACGAAGCGTACAAACGCGTGCAAGTGATGCGCCTCGCGGGTTACCTGCTTGATGCGCCGTTGCAGCTCACTGCCCAGCCGGTCACCGGCCAGCATTGCC‑GTGCGGTCGCCATggg < 2:18302/149‑1 (MQ=255)
gCTCAGCCAGTTCCTCTGGCAACGGCACGAAGCGTACAAACGCGTGCAAGTGATGCGCCTCGCGGGTTACCTGCTTGATGCGCCGTTGCAGCTCACTGCCCAGCCGGTCACCGGCCAGCATTGCC‑GTGCGGTGGGCCTggggggcggg > 7:368926/1‑141 (MQ=255)
tctGGCAACGGCACGAAGCGTACAAACGCGTGCAAGTGATGCGCCTCGCGGGTTACCTGCTTGATGCGCCGTTGCAGCTCACTGCCCAGCCGGTCACCGGCCAGCATTGCC‑GTGGGGTGGGCAAGGGCGGCGCGCCACACCCcatcat > 1:108468/1‑148 (MQ=255)
tctGGCAACGGCACGAAGCGTACAAACGCGTGCAAGTGATGCGCCTCGCGGGTTACCTGCTTGATGCGCCGTTGCAGCTCACTGCCCAGCCGCTCACCGGCCAGCATTGCC‑GTGCCATCGCCATGGGCGACCCGCCACAACACATcct > 2:276703/1‑146 (MQ=255)
ctGGCAACGGCACGAAGCGTACAAACGCGTGCAAGTGATGCGCCTCGCGGGTTACCTGCTTGATGCGCCGTTGCAGCTCACTGCCCAGCCGGTCACCGGCCAGCATTGCC‑GTGCGGGCGCCAATGGGGACGCGCCCCAGcccaagaa > 6:255642/1‑140 (MQ=255)
aGCGTACAACCGCGTGCAAGTGATGCGCCGCGCGGGTTACCGGCTTTATGCGCCGTTGCTGCTCACTGCCCAGCCGGTCACCGGCCAGAATTGCC‑GTGCGGTCGCCTTGGGCTACGCGCCACAGCACTTCATACAGCAGGTTCCAgc < 2:136884/147‑1 (MQ=255)
aCAAACGCGTGCAAGTGATGCGCCTCGCGGGTTACCTGCTTGATGCGCCGTTGCAGCTCACTGCCCAGCCGGTCACCGGCCAGCATTGCC‑GTGCGGTCGCCAAGGGCGCCGCGCCCCAGCCCGTAATACAGCAGGGTCCACCgcggcg > 7:214701/1‑147 (MQ=255)
tGCTAGTTATGCCCCGCGGGGGTAACCTGCTTTTGGCGCGTTTCCCCCACACT‑CCCCCCCGGGCCCCCGCCAACATTGCCGGGGCGGCCCCAAGGGGCGACGCGCCACAGCACTTCATACAGCAGGTTCCAGCGCTGCTCGCCACGGt < 6:59775/148‑1 (MQ=255)
ggTTACCTGCTTGATGCGCCGTTGCAGCTCACTACCCAGCCGGTCACCGGCCAGCATTGCC‑GTGCGGTCGCCATGGGCGACGCGCCACAGCACTTCATACAGCAGGTTCCAGCGCTGCTCGCCACGGTAGCGAGAGGCCTGCTCCAAc < 6:191928/148‑1 (MQ=255)
ttACCTGCTTGATGCGCCGTTGCAGCTCACTGCCCAGCCGGTCACCGGCCAGCATTGCC‑GTGCGGTCGCCAAGGGCGCCCCGCCCCACCACATAAAAAACCACGTTACACCGCTGCTCGTCACCGTAGCGAGAGGCCAGCGCCAAcag > 6:97808/1‑146 (MQ=255)
ttACCTGCTTGATGCGCCGTTGATGTTCACTGCCAAGCCGGGCACCGGCCTGCATTGCT‑TTGCGTGCGCAATGGGGGACGCGCCACAGCACTTCATACTGCAGGTTCCAGCGCTGCTCGCCACGTTAGCGAGAGGCCTGCTCCAACTgg < 2:267435/149‑1 (MQ=255)
gttttaTGCGCCGTGGCTGTTCACTGCCCAGCGGGTCACGGGCATGATTTGCG‑GTGGGGTGGCCTTGGGCTACGCGCCACAGCACTTCATACAGCAGGTTCCAGCGCTGCTCGCCACGGTAGCGAGAGGCCTGCTCCAACTGGCTca < 4:263097/142‑1 (MQ=255)
cTTGATGCGCCGTTGCAGCTCACTGCCCAGCCGGTCACCGGCCAGCATTGCC‑GTGGGGGGGCCAAGGGCGCCGCGCCCCCGCCCATAATACAGCAGGTTACAGCGCTGCTCGCCACCGGAGCGAGAGGCCGGCTCCAACAGGGTcag > 2:75961/1‑147 (MQ=255)
cGTTGCAGCTCACTGCCCAGCCGGTCACCGGCCAGCATTGCC‑GTGCGGTCGCCATGGGCGACGCGCCACAGCACTTCATACAGCAGGTTCCAGCGCTGCTCGCCACGGTAGCGAGAGGCCTGCTCCAACTGGCGCAGCAGTGCGGCCgg < 1:59445/149‑1 (MQ=255)
gTTGCAGCTCACTGCCCAGCCGGTCACCGGCCAGCATTGCC‑GTGCGGGGGGCAAGGGCGGCGCGCCCCCCCCCGTCAAACAGCAGGGTGCAGCGCGGCTCGCCCCCGGAGCGCGAGGGCGGCGCCAACAGGCTGAGCAGTGGGGcccg > 8:166691/1‑146 (MQ=255)
aGCTCACTGCCCAGCCGGTCACCGGCCAGCATTGCC‑GTGCGGTCGCCATGGGCGACGCGCCACAGCACTTCATACAGCAGGTTCCAGCGCTGCTCGCCACGGTAGCGAGAGGCCTGCTCCAACTGGCTCAGCAGTGCGGCCGGGAC‑ttt < 4:358164/149‑1 (MQ=255)
aCTGCCCCGCGGGGCCCCGGCCAGCTTTGCG‑GGGGGGGCCCCAGGGGCTACGCGCCACAGCACTTCATACAGCAGGTTCCAGCGCTGCTCGCCACGGTAGCGAGAGGCCTGCTCCAACTGGCTCAGCAGTGCGGCCGGGAC‑TTTgg < 5:255642/146‑1 (MQ=255)
gCCCAGCCGGTCACCGGCCAGCATTGCC‑GTGCGGTGGCCATGGGCGACGCGCCCCAGCACGTCATACAGGATGTTGCCGCGCGGCGCGCCCCGGTAGCGCGAGGGCGGCTCCAACGGGGGGAGCAGGGGGGCGGGGTCTTTTGGCCCg > 6:402342/1‑148 (MQ=255)
ccAGCCGGTCACCGGCCAGCATTGCC‑GTGCGGTCGCCATTGGCGACGCGCCACACCACTTAATAAAGCAGGTTACACCGCTGCTCGCCACCGTAGCGAGAGGCCTGCTCCAACAGGCTCAGCACTGCGGCCGGGAC‑TTTTGCCCGGaa > 2:22022/1‑148 (MQ=255)
aGCCGGTCACCGGCCAGCATTGCC‑GTGCGGTCGCCATGGGCGACGCGCCACAGCACTTCATACAGCAGGTTCCAGCGCTGCTCGCCACGGTAGCGAGAGGCCTGCTCCAACTGGCTCAGCAGTGCGGCCGGGAC‑TTTGGCCCGGAAAgg < 2:108468/149‑1 (MQ=255)
gCCGGTCACCGGCCAGCATTGCC‑GTGCGGTCGCCATGGGCGACGCGCCACAGCACTTCATACAGCAGGTTCCAGCGCTGCTCGCCACGGTAGCGAGAGGCCTGCTCCAACTGGCTCAGCAGTGCGGCCGGGAC‑TTTGGCCCGGAAAgg < 8:214701/148‑1 (MQ=255)
aCCGGCCACATTTGCG‑GGGCGGGCGCCATGGGCGACGCGCCACAGCACTTCATACAGCAGGTTCCAGCGCTGCTCGCCACGGTAGCGAGAGGCCTGCTCCAACTgg < 3:186683/106‑1 (MQ=255)
cATGGCC‑GGGCGGTCGCCATGGGCGACGCGCCACAGCACTTCATACAGCAGGTTCCAGCGCTGCTCGCCACGGTAGCGAGAGGCCTGCTCCAACTGGCTCAGCAGTGCGGCCGGGAC‑TTTGGCCCGGAAAGGGCCCGGCCCGTCAggcg < 1:49517/149‑1 (MQ=255)
aTTGCC‑GTGCGGTCGCCATGGGCGACGCGCCACAGCACTTCATACAGCAGGTTCCAGCGCTGCTCGCCACGGTAGCGAGAGGCCTGCTCCAACTGGCTCAGCAGTGCGGCCGGGAC‑TTTGGCCCGGAAAGGGCCCGGCCCGTCAggcg < 7:293743/148‑1 (MQ=255)
ttGCC‑GTGCGGTCGCCATGGGCGACGCGCCACAGCACTTCATACAGCAGGTTCCAGCGCTGCTCGCCACGGTAGCGAGAGGCCTGCTCCAACTGGCTCAGCAGTGCGGCCGGGAC‑TTTGGCCCGGAAAGGGCCCGGCCCGTCAggcggc < 2:247200/149‑1 (MQ=255)
gTGCGGCCGCCATGGGCGACGCGCCACAGCACTTCATACAGCAGGTTCCAGCGCTGCTCGCCACGGTAGCGAGAGGCCTGCTCCAACTGGCTCAGCAGTGCGGCCGGGAC‑TTTGGCCCGGAAAGGGCCCGGCCCGTCAGGCGGCGCTg < 8:368926/148‑1 (MQ=255)
ggTCGCCATGGGCGACGCGCCACAGCACTTCATACAGCAGGTTCCAGCGCTGCTCGCCACGGTAGCGAGAGGCCTGCTCCAACTGGCTCAGCAGTGCGGCCGGGAC‑TTTGGCCCGGAAAGGGCCCGGCCCGTCAGGCGGCGCTGCCgg > 5:400629/1‑148 (MQ=255)
gTCGCCATGGGCGACGCGCCACAGCACTTCATACAGCAGGTTCCAGCGCTGCTCGCCACGGTAGCGAGAGGCCTGCTCCAACTGGCTCAGCAGTGCGGCCGGGAC‑TTTGGCCCGGAAAGGGCCCGGCCCGTCAGGCGGCGCTGCCGgca > 3:47448/1‑149 (MQ=255)
|
CTGCAAGTGCTCAGCCAGTTCCTCTGGCAACGGCACGAAGCGTACAAACGCGTGCAAGTGATGCGCCTCGCGGGTTACCTGCTTGATGCGCCGTTGCAGCTCACTGCCCAGCCGGTCACCGGCCAGCATTGCC‑GTGCGGTCGCCATGGGCGACGCGCCACAGCACTTCATACAGCAGGTTCCAGCGCTGCTCGCCACGGTAGCGAGAGGCCTGCTCCAACTGGCTCAGCAGTGCGGCCGGGAC‑TTTGGCCCGGAAAGGGCCCGGCCCGTCAGGCGGCGCTGCCGGCA > NC_002947_CJ‑RC/3323464‑3323750
|
| 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
