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 |
4,586,142 |
+G |
intergenic (+118/+97) |
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 | 4,586,140 | 1 | . | G | 87.5%
| 44.9
/ 1.0
| 16 | intergenic (+116/+99) | PP_4061/PP_4063 | hypothetical protein/long‑chain fatty acid‑‑CoA ligase |
| Reads supporting (aligned to +/- strand): ref base . (0/2); new base G (1/13); total (1/15) |
| 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 |
GCCGAGCCAGGAGCCACCGGTGAAGGCTTAAGGGTAGACCACGGCACCGGCGTGAACAGCTGATCTGCGCTGCTCCATTGAAAGGTTGAGGATGACCGGGTGCTTGGCAAGGTGAAGATCTTGCATTGATCGGGCCGGCCTC‑TCTGC‑GG‑TAAACCCGCTCCTACCAGGG‑A‑CGTGCCGGCCTTGAATGCGGCGCTGCCCCTGGTAGGAGCGGGTTTACCC > NC_002947_CJ‑RC/4585994‑4586212
|
gccgAGCCAGGAGCCACCGGTGGAGGCTTAAGGGTAGACCACGGCACCGGCGTGAACAGCTGATCTGCGCTGCTCCATTGAAAGGTTGAGGATGACCGGGTGCTTGGCAAGGTGAAGATCTTGCATTGATCGGGCCGGCCTC‑TTCGC‑gg > 7:321335/1‑149 (MQ=255)
ccAGGAGCCACCGGTGAAGGCTTAAGGGTAGACCACGGCACCGGCGTGAACAGCTGATCTGCGCTGCTCCATTGAAAGGTTGAGGATGACCGGGTGCTTGGCAAGGTGAAGATCTTGCATTGATCGGGCCGGCCTC‑TTCGC‑gggtaaa < 1:66482/148‑6 (MQ=255)
ccGGTGAAGGCTTAAGGGTAGACCACGGCACCGGCGTGAACAGCTGATCTGCGCTGCTCCATTGAAAGGTTGAGGATGACCGGGTGCTTGGCAAGGTGAAGATCTTGCATTGATCGGGCCGGCCTC‑TTCGCGGG‑TAAACCCGCTCCTa > 5:359440/1‑148 (MQ=255)
aGGCTTAAGGGTAGACCACGGCACCGGCGTGAACAGCTGATCTGCGCTGCTCCATTGAAAGGTTGAGGATGACCGGGTGCTTGGCAAGGTGAAGATCTTGCATTGATCGGGCCGGCCTC‑TTCGCGGG‑TAAACCCGCTCCTACCAGGG‑a < 3:188965/148‑1 (MQ=255)
tAGACCACGGCACCGGCGTGAACAGCTGATCTGCGCTGCTCCATTGAAAGGTTGAGGATGACCGGGTGCTTGGCAAGGTGAAGATCTTGCATTGATCGGGCCGGCCTC‑TTCGCGGG‑TAAACCCGCTCCTACCAGGG‑ACCGTGCCGGcc < 6:359440/148‑1 (MQ=39)
tAGACCACGGCACCGGCGTGAACAGCTGATCTGCGCTGCTCCATTGAAAGGTTGAGGATGACCGGGTGCTTGGCAAGGTGAAGATCTTGCATTGATCGGGCCGGCCTC‑TTCGCGGG‑TAAACCCGCTCCTACCAGGG‑ACCGTGCCGGcc < 3:264493/148‑1 (MQ=39)
gACCACGGCACCGGCGTGAACAGCTGATCTGCGCTGCTCCATTGAAAGGTTGAGGATGACCGGGTGCTTGGCAAGGTGAAGATCTTGCATTGATCGGGCCGGCCTC‑TTCGCGGG‑TAAACCCGCTCCTACCAGGG‑ACCGTGCCGGCCtt < 3:347131/148‑1 (MQ=39)
aCCACGGCACCGGCGTGAACAGCTGATCTGCGCTGCTCCATTGAAAGGTTGAGGATGACCGGGTGCTTGGCAAGGTGAAGATCTTGCATTGATCGGGCCGGCCTC‑TTCGCGGG‑TAAACCCGCTCCTACCAGGG‑ACCGTGCCGGCCTTg < 6:136752/148‑1 (MQ=39)
ccACGGCACCGGCGTGAACAGCTGATCTGCGCTGCTCCATTGAAAGGTTGAGGATGACCGGGTGCTTGGCAAGGTGAAGATCTTGCATTGATCGGGCCGGCCTC‑TTCGCGGG‑TAAACCCGCTCCTACCAGGG‑ACCGTGCCGGCCTTGa < 2:169300/148‑1 (MQ=39)
ctgCACCGGCGTGAACAGCCGATCTGCGCTGCTCCATTGAAAGTTTGAGGATGACCGGGTGCTTGGCAAGGTGAAGATCTTGCATTGATCGGGCCGGCCTC‑TTCGCGGG‑TAAACCCGCTCCTACCAGGG‑ACCGTGCCGGCCTTGAATg < 3:56829/146‑1 (MQ=38)
aaCAGCTGATCTGCGCTGCTCCATTGAAAGGTTGAGGATGACCGGGTGCTTGGCAAGGTGAAGATCTTGCATTGATCGGGCCGGCCTC‑TTCGCGGG‑TAAACCCGCTCCTACCAGGG‑ACCGTGCCGGCCTTGAATGCGGCGCTGcccc < 1:346281/147‑1 (MQ=39)
aaCAGCTGATCTGCGCTGCTCCATTGAAAGGTTGAGGATGACCGGGTGCTTGGCAAGGTGAAGATCTTGCATTGATCGGGCCGGCCTC‑TTCGCGGG‑TAAACCCGCTCCTACCAGGG‑ACCGTGCCGGCCTTGAATGCGGCGCTGCCCCt < 6:307148/148‑1 (MQ=39)
cAGCTGATCTGCGCTGCTCCATTGAAAGGTTGAGGATGACCGGGTGCTTGGCAAGGTGAAGATCTTGCATTGATCGGGCCGGCCTC‑TTCGCGGG‑TAAACCCGCTCCTACCAGGG‑ACCGTGCCGGCCTTGAATGCGGCGCTGCCCCTgg < 1:14435/148‑1 (MQ=39)
cAGCTGATCTGCGCTGCTCCATTGAAAGGTTGAGGATGACCGGGTGCTTGGCAAGGTGAAGATCTTGCATTGATCGGGCCGGCCTC‑TTCGCGGG‑TAAACCCGCTCCTACCAGGG‑ACCGTGCCGGCCTTGAATGCGGCGCTGCCCCTGGt < 7:209928/149‑1 (MQ=39)
aGCTGATCTGCGCTGCTCCATTGAAAGGTTGAGGATGACCGGGTGCTTGGCAAGGTGAAGATCTTGCATTGATCGGGCCGGCCTC‑TTCGCGGG‑TAAACCCGCTCCTACCAGGG‑ACCGTGCCGGCCTTGAATGCGGCGCTGCCCCTGGTa < 7:281605/149‑1 (MQ=39)
gCTGATCTGCGCTGCTCCATTGAAAGGTTGAGGATGACCGGGTGCTTGGCAAGGTGAAGATCTTGCATTGATCGGGCCGGCCTC‑TTCGCGGG‑TAAACCCGCTCCTACCAGGG‑ACCGTGCCGGCCTTGAATGCGGCGCTGCCCCTGGTa < 2:38769/148‑1 (MQ=39)
ctCCATTTAATGGTTTAGGATCACCGGGTGCTTGGCAAGGTGAAGATGTTGCATTTATCGGGCCGGCCTC‑TTCGC‑GGCTAAACCCGCTCCTACCAGGG‑ACCGTGCCGGCCTTTAATGCGGCGCTGCCCCTGGTAGGAGCGGGTTTAcc < 2:280662/148‑1 (MQ=25)
ctCCATTTAATGGTGGAGGATGACCGGGTGCTTGGCATGGTTATGATCTTGCATTGACCGGGCCGGCCGCTTCGGG‑GG‑TAAACCCGCTCCTACCCGGGCC‑CGTGCGGGCCTTGATTGCGGGGGTGCCCCTGGTAGGAGCGGGTTTAccc < 8:321335/149‑1 (MQ=255)
|
GCCGAGCCAGGAGCCACCGGTGAAGGCTTAAGGGTAGACCACGGCACCGGCGTGAACAGCTGATCTGCGCTGCTCCATTGAAAGGTTGAGGATGACCGGGTGCTTGGCAAGGTGAAGATCTTGCATTGATCGGGCCGGCCTC‑TCTGC‑GG‑TAAACCCGCTCCTACCAGGG‑A‑CGTGCCGGCCTTGAATGCGGCGCTGCCCCTGGTAGGAGCGGGTTTACCC > NC_002947_CJ‑RC/4585994‑4586212
|
| Alignment Legend |
|---|
Aligned base mismatch/match (shaded by quality score): ATCG/ATCG < 3 ≤ ATCG/ATCG < 14 ≤ ATCG/ATCG < 21 ≤ ATCG/ATCG < 36 ≤ ATCG/ATCG |
Unaligned base: atcg Masked matching base: atcg Alignment gap: ‑ Deleted base: ‑ |
GATK/CNVnator alignment
N/A
