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 |
4,586,163:1 |
+C |
100% |
intergenic (+139/+76) |
PP_4061 → / ← PP_4063 |
hypothetical protein/long‑chain fatty acid‑‑CoA ligase |
|
| |
seq id |
position |
ref |
new |
freq |
score (cons/poly) |
reads |
annotation |
genes |
product |
| * | NC_002947_CJ‑RC | 4,586,163 | 1 | . | C | 88.5%
| 78.1
/ 4.5
| 26 | intergenic (+139/+76) | PP_4061/PP_4063 | hypothetical protein/long‑chain fatty acid‑‑CoA ligase |
| Reads supporting (aligned to +/- strand): ref base . (1/2); new base C (7/16); total (8/18) |
| Fisher's exact test for biased strand distribution p-value = 1.00e+00 |
| Kolmogorov-Smirnov test that lower quality scores support variant p-value = 8.52e-01 |
| Rejected as polymorphism: Variant not supported by required number of reads on each strand. |
CGGCACCGGCGTGAACAGCTGATCTGCGCTGCTCCATTGAAAGGTTGAGGATGACCGGGTGCTTGGCAAGGTGAAGATCTTGCATTGATCGGGCCGGCCTCTCTGC‑GGTAAACCCGCTCCTACCAGGGA‑C‑GTGCCGGCCTTGAATG‑CGGCGCTGCCCCTGGTAGGAGCGGGTTTACCCGCGAAGAGGCCGGCCGCGCCAGCACATCAACCCGCAGATGCAGCCGCAATCTCCGCCACACTGATCTCACGCATGCGGAACTTCTGCACCTTGC > NC_002947_CJ‑RC/4586035‑4586306
|
cGGCACCGGCGTGAACAGCTGATCTGCGCTGCTCCATTGAAAGGTTGAGGATGACCGGGTGCTTGGCAAGGTGAAGATCTTGCATTGATCGGGCCGGCCTCTTCGCGGGTAAACCCGCTCCTACCAGGGACC‑GTGCCGGCCTTGAATg < 8:207864/148‑1 (MQ=39)
cGGCACCGGCGTGAACAGCTGATCTGCGCTGCTCCATTGAAAGGTTGAGGATGACCGGGTGCTTGGCAAGGTGAAGATCTTGCATTGATCGGGCCGGCCTCTTCGCGGGTAAACCCGCTCCTACCAGGGACC‑GTGCCGGCCTTGAATg < 7:119807/148‑1 (MQ=39)
gCACCGGCGTGAACAGCTGATCTGCGCTGCTCCATTGAAAGGTTGAGGATGACCGGGTGCTTGGCAAGGTGAAGATCTTGCATTGATCGGGCCGGCCTCTTCGCGGGTAAACCCGCTCCTACCAGGGACC‑GTGCCGGCCTTGAATg‑cgg < 3:342531/149‑1 (MQ=39)
gCACCGGCGTGAACAGCTGATCTGCGCTGCTCCATTGAAAGGTTGAGGATGACCGGGTGCTTGGCAAGGTGAAGATCTTGCATTGATCGGGCCGGCCTCTTCGCGGGTAAACCCGCTCCTACCAGGGACC‑GTGCCGGCCTTGAATg‑cgg < 4:190654/149‑1 (MQ=39)
aCAGCTGATCTGCGCTGCTCCATTGAAAGGTTGAGGATGACCGGGTGCTTGGCAAGGTGAAGATCTTGCATTGATCGGGCCGGCCTCTTCGC‑GGGAAACCCGCTCCTACCAGGGACC‑GTGCCGGCCTTGAATG‑CGGCGCTGCCCCTg < 7:108566/147‑1 (MQ=255)
aGCTGATCTGCGCTGCTCCATTGAAAGGTTGAGGATGACCGGGTGCTTGGCAAGGTGAAGATCTTGCATTGATCGGGCCGGCCTCTTCGCGGGTAAACCCGCTCCTACCAGGGACC‑GTGCCGGCCTTGAATG‑CGGCGCTGCCCCTGGTa < 3:319008/149‑1 (MQ=39)
aGCTGATCTGCGCTGCTCCATTGAAAGGATGAGGATGACCGGGTGCTTGGCAAGGTGAAGATCTTGCATTGATCGGGCCGGCCTCTTCGCGGGTAAACCCGCTCCTACCAGGGACC‑GTGCCGGCCTTGAATG‑CGGCGCTGCCCCTGGTa < 3:373802/149‑1 (MQ=38)
gCTGATCTGCGCTGCTCCATTGAAAGGTTGAGGATGACCGGGTGCTTGGCAAGGTGAAGATCTTGCATTGATCGGGCCGGCCTCTTCGCGGGTAAACCCGCTCCTACCAGGGACC‑GTGCCGGCCTTGAATG‑CGGCGCTGCCCCTGGTa < 7:63489/148‑1 (MQ=39)
aTCTGCGCTGCTCCATTGAAAGGTTGAGGATGACCGGGTGCTTGGCAAGGTGAAGATCTTGCATTGATCGGGCCGGCCTCTTCGCGGGTAAACCCGCTCCTACCAGGGACC‑GTGCCGGCCTTGAATG‑CGGCGCTGCCCCTGGTAgg < 7:340963/146‑1 (MQ=39)
cgcTGCTCCATTGAAAGGTTGAGGATGACCGGGTGCTTGGCAAGGTGAAGATCTTGCATTGATCGGGCCGGCCTCTTCGCGGGTAAACCCGCTCCTACCAGGGACC‑GTGCCGGCCTTGAATG‑CGGCGCTGCCCCTGGTAGGAg < 8:420330/143‑1 (MQ=38)
cgcTGCTCCATTGAAAGGTTGAGGATGACCGGGTGCTTGGCAAGGTGAAGATCTTGCATTGATCGGGCCGGCCTCTTCGCGGGTAAACCCGCTCCTACCAGGGACC‑GTGCCGGCCTTGAATG‑CGGCGCTGCCCCTGGTAGGAGc < 3:63292/144‑1 (MQ=38)
gctgctCCATTGAAAGGTTGAGGATGACCGGGTGCTTGGCAAGGTGAAGATCTTGCATTGATCGGGCCGGCCTCTTCGCGGGTAAACCCGCTCCTACCAGGGACC‑GTGCCGGCCTTGAATG‑CGGCGCTGCCCCTGGTAGGAGCGGGttt < 2:36866/149‑1 (MQ=38)
tgctCCATTGAAAGGTTGAGGATGACCGGGTGCTTGGCAAGGTGAAGATCTTGCATTGATCGGGCCGGCCTCTTCGCGGGTAAACCCGCTCCTACCAGGGACC‑GTGCCGGCCTTGAATG‑CGGCGCTg > 8:263212/1‑127 (MQ=38)
tgctCCATTGAAAGGTTGAGGATGACCGGGTGCTTGGCAAGGTGAAGATCTTGCATTGATCGGGCCGGCCTCTTCGCGGGTAAACCCGCTCCTACCAGGGACC‑GTGCCGGCCTTGAATG‑CGGCGCTg < 7:263212/127‑1 (MQ=38)
ctCCATTGAAAGGTTGAGGATGACCGGGTGCTTGGCAAGGTGAAGATCTTGCATTGATCGGGCCGGCCTCTTCGCGGGTAAACCCGCTCCTACCAGGGACC‑GTGCCGGCCTTGAATG‑CGGCGCTGCCCCTGGTAGGAGCGGGTTTAcc < 8:57953/148‑1 (MQ=38)
ccATTGAAAGGTTGAGGATGACCGGGTGCTTGGCAAGGTGAAGATCTTGCATTGAGCGGGCCGGCCTCTTCGCGGGTAAACCCGCTCCTACCAGGGACC‑GGGCCGGCCTTGAATG‑CGGCGCTGCCCCTGGTAGGAGCGGGTTTACCcgc < 1:315070/149‑1 (MQ=37)
tAAACCCGCTCCTACCAGGGACC‑GTGCCGGCCTTGAATG‑CGGCGCTGCCCCTGGTAGGAGCGGGTTTACCCGCGAAGAGGCCGGCCGCGCCAGCACATCAACCCGCAGATGCAGCCGCAATCTCCGCCACACTGATCTCACGCATGCg > 8:35771/1‑148 (MQ=255)
aaCCCGCTCCTACCAGGGG‑CAGCGCC‑GCATTCAAGGCCGGCACGGTCCCTGGTAGGAGCGGGTTTACCCGCGAAGAGGCCGGCCGAGCCAGCACATCAACCCGCAGATGCAGCCGCAATCTCCGCCACACTGATCTCACGCATGCgg > 7:239143/1‑147 (MQ=18)
cccGCTCCTACCAGGGACC‑GTGCCGGCCTTGAATG‑CGGCGCTGCCCCTGGTAGGAGCGGGTTTACCCGCGAAGAGGCCGGCCGCGCCAGCACATCAACCCGCAGATGCAGCCGCAATCTCCGCCACACTGATCTCACGCATGCGGAAc > 8:233006/1‑148 (MQ=255)
ccGCTCCTACCAGGGACC‑GTGCCGGCCTTGAATG‑CGGCGCTGCCCCTGGTAGGAGCGGGTTTACCCGCGAAGAGGCCGGCCGCGCCAGCACATCAACCCGCAGATGCAGCCGCAATCTCCGCCACACTGATCTCACGCATGCGGAACtt > 2:213403/1‑149 (MQ=255)
gCTCCTACCAGGGACC‑GTGCCGGCCTTGAATG‑CGGCGCTGCCCCTGGTAGGAGCGGGTTTACCCGCGAAGAGGCCGGCCGCGCCAGCACATCAACCCGCAGATGCAGCCGCAATCTCCGCCACACTGATCTCACGCATGCGGAACTTCt > 3:374534/1‑149 (MQ=255)
cTCCTACCAGGGA‑CCGTGCCGGCCTTGAATG‑CGGCGCTGCCCCTGGTAGGAGCGGGTTTACCCGCGAagaggccggcccgatcaatgcaagatcttcaccttgccaagcacccggtcatcctcaacctttcaatggagcagcg < 5:182382‑M2/143‑77 (MQ=255)
tACCAGGGACC‑GTGCCGGCCTTGAATG‑CGGCGCTGCCCCTGGTAGGAGCGGGTTTACCCGCGAAGAGGCCGGCCGCGCCAGCACATCAACCCGCAGATGCAGCCGCAATCTCCGCCACACTGATCTCACGCATGCGGAACTTCTGCAcc > 1:125621/1‑149 (MQ=255)
cAGGGA‑CCGTGCCGGCCTTGAATG‑CGGCGCTGCCCCTGGTAGGAGCGGGTTTACCCGCGAagaggccggcccgatcaatgcaagatcttcaccttgccaagcacccggtcatcctcaacctttcaatggagcagcgcagatcagctgt < 6:5610‑M2/148‑89 (MQ=255)
aGGGACC‑GTGCCGGCCTTGAATG‑CGGCGCTGCCCCTGGTAGGAGCGGGTTTACCCGCGAAGAGGCCGGCCGCGCCAGCACATCAACCCGCAGATGCAGCCGCAATCTCCGCCACACTGATCTCACGCATGCGGAACTTCTGCACCtag > 5:387793/1‑146 (MQ=255)
aGGGACC‑GTGCCGGCCTTGAATG‑CGGCGCTGCCCCTGGTAGGAGCGGGTTTACCCGCGAAGAGGCCGGCCGCGCCAGCACATCAACCCGCAGATGCAGCCGCAATCTCCGCCACACTGATCTCACGCATGCGGAACTTCTGCACCTTGc < 1:213403/149‑1 (MQ=255)
|
CGGCACCGGCGTGAACAGCTGATCTGCGCTGCTCCATTGAAAGGTTGAGGATGACCGGGTGCTTGGCAAGGTGAAGATCTTGCATTGATCGGGCCGGCCTCTCTGC‑GGTAAACCCGCTCCTACCAGGGA‑C‑GTGCCGGCCTTGAATG‑CGGCGCTGCCCCTGGTAGGAGCGGGTTTACCCGCGAAGAGGCCGGCCGCGCCAGCACATCAACCCGCAGATGCAGCCGCAATCTCCGCCACACTGATCTCACGCATGCGGAACTTCTGCACCTTGC > NC_002947_CJ‑RC/4586035‑4586306
|
| Alignment Legend |
|---|
Aligned base mismatch/match (shaded by quality score): ATCG/ATCG < 3 ≤ ATCG/ATCG < 14 ≤ ATCG/ATCG < 27 ≤ ATCG/ATCG < 36 ≤ ATCG/ATCG |
Unaligned base: atcg Masked matching base: atcg Alignment gap: ‑ Deleted base: ‑ |
GATK/CNVnator alignment
N/A
