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 |
|
A0 F0 I1 R1
|
59 |
79.3 |
3391134 |
98.6% |
3343658 |
146.3 |
Breseq alignment
BRESEQ :: Evidence
|
| evidence |
seq id |
position |
mutation |
annotation |
gene |
description |
| RA |
NC_002947_CJ‑RC |
1,499,508 |
+C |
intergenic (+85/‑79) |
trpS → / → zapE |
tryptophan‑‑tRNA ligase/nucleoside triphosphate hydrolase domain‑containing protein |
|
| |
seq id |
position |
ref |
new |
freq |
score (cons/poly) |
reads |
annotation |
genes |
product |
| * | NC_002947_CJ‑RC | 1,499,506 | 1 | . | C | 100.0%
| 33.1
/ NA
| 11 | intergenic (+83/‑81) | trpS/zapE | tryptophan‑‑tRNA ligase/nucleoside triphosphate hydrolase domain‑containing protein |
| Reads supporting (aligned to +/- strand): ref base . (0/0); new base C (10/1); total (10/1) |
AGGCTGCCAAACGGTGGGAGCGGGCGTGCCCGCGAAACAGGCGCCGCGGTGCATGGCCACGGCTTTGCCGGTGTT‑TCGGGCACG‑CCGCTCCCACAGACTGATTGCCATTAAGCGGGCCTATCGCTACAGTGACGGCCCGTTTTTTGTTGCCTCGCTAACGAATCATGACTCCCTTAGAACGCTATCAAGCAGATCTGAAACGTCCCGACTTCTTCCATGACGCGGCG > NC_002947_CJ‑RC/1499423‑1499649
|
aGGCTGCCAACCGGGGGGAGCGGGCGTCCCCGCGATTCTGGGCCCGGGGTGCAGGGCACGGGTTTTGCCGTTGTTCGCTGGCACGCCCGCTCCCACAGACTGATTGCCTTTAAGCGGGCCTATCGCTACAGTGACGGCCCGtttttgt < 2:359986/148‑3 (MQ=255)
cccGCGAAACAGGCGCCGCGGTGCATGGCACCGGCTTTGCCGGTGTTCGCGGGCCCGCCCGCGCCCACAGACTGATTGCCATTAAGCGGGCCTATCGCTACAGTGACGGCCCGGTTTTTGTTGCCTCGCTTACGAATCATGACTGCCtt > 1:376422/1‑149 (MQ=25)
ccGCGAAACAGGCGCCGCGGTGCATGGCACCGGCTTTGCCGGTGTTCGCGGGCACGCCCGCTCCCACAGACTGATTGCCATTAAGCGGGCCTATCGCTACAGTGACGGCCCGTTTTTTGTTGCCTCGCTAACGAATCATGACTCCCt > 1:317336/1‑147 (MQ=37)
cgcgAAACAGGCGCCGCGGTGCATGGCACCGGCTTTGCCGGTGTTCGCGGGCACGCCCGCTCCCACAGACTGATTGCCATTAAGCGGGCCTATCGCTACAGTGACGGCCCGTTTTTTGTTGCCTCGCTAACGAATCATGACTCCCt > 4:7535/1‑146 (MQ=37)
gcgAAACAGGCGCCGCGGTGCATGGCACCGGCTTTGCCGGTGTTCGCGGGCACGCCCGCTCCCACAGACTGATTGCCATTAAGCGGGCCTATCGCTACAGTGACGGCCCGTTTTTTGTTGCCTCGCTAACGAATCATGACTCCCTTAg > 5:145850/1‑148 (MQ=37)
ggCGCCGCGGTGCATGGCACCGGCTTTGCCGGTGTTCGCGGGCACGCCCGCTCCCACAGACTGATTGCCATTAAGCGGGCCTATCGCTACAGTGACGGCCCGTTTTTTGTTGCCTCGCTAACGAATCATGACTCCCTTAGAACGCTAt > 3:262960/1‑148 (MQ=37)
aTGGCACCGGCTTTGCCGGTGTTCGCGGGCACGCCCGCTCCCACAGACTGATTGCCATTAAGCGGGCCTATCGCTACAGTGACGGCCCGTTTTTTGTTGCCTCGCTAACGAATCATGACTCCCTTAGAACGCTATCAAGCAGATCTGa > 5:412496/1‑148 (MQ=38)
tggcaccGGCTTTGCCGGTGTTCGCGGGCACGCCCGCTCCCACAGACTGATTGCCATTAAGCGGGCCTATCGCTACAGTGACGGCCCGTTTTTTGTTGCCTCGCTAACGAATCATGACTCCCTTAGAACGCTATCAAGCAGATCTGaaa > 2:383510/7‑149 (MQ=38)
ccGGCTTTGCCGGTGTTCGCGGGCACGCCCGCTCCCACAGACTGATTGCCATTAAGCCGGCCTATCGCTACAGTGACGGCCCGGTTTTTGTTGCCTCGCTAACGCAGCATGACTCCCTTAGAACGCTATCAAGGAGATCTGAAACGTcc > 5:62340/2‑149 (MQ=37)
ccGGTGTTCGCGGGCACGCCCGCTCCCACAGACTGATTGCCATTAAGCGGGCCTATCGCTACAGTGACGGCCCGTTTTTTGTTGCCTCGCTAACGAATCATGACTCCCTTAGCACGCTATCAAGCAGATCTGAAACGTCCCGActtctt > 7:291313/1‑149 (MQ=255)
gCACGCCCGCTCCCACAGACTGATTGCCATTAAGCGGGCCTATCGCTACAGTGACGGCCCGTTTTTTGTTGCCTCGCTAACGAATCATGACTCCCTTAGAACGCTATCAAGCAGATCTGAAACGTCCCGACTTCTTCCATGACgcggcg > 5:61246/1‑149 (MQ=255)
|
AGGCTGCCAAACGGTGGGAGCGGGCGTGCCCGCGAAACAGGCGCCGCGGTGCATGGCCACGGCTTTGCCGGTGTT‑TCGGGCACG‑CCGCTCCCACAGACTGATTGCCATTAAGCGGGCCTATCGCTACAGTGACGGCCCGTTTTTTGTTGCCTCGCTAACGAATCATGACTCCCTTAGAACGCTATCAAGCAGATCTGAAACGTCCCGACTTCTTCCATGACGCGGCG > NC_002947_CJ‑RC/1499423‑1499649
|
| Alignment Legend |
|---|
Aligned base mismatch/match (shaded by quality score): ATCG/ATCG < 3 ≤ ATCG/ATCG < 14 ≤ ATCG/ATCG < 15 ≤ ATCG/ATCG < 32 ≤ ATCG/ATCG < 36 ≤ ATCG/ATCG |
Unaligned base: atcg Masked matching base: atcg Alignment gap: ‑ Deleted base: ‑ |
GATK/CNVnator alignment
BRESEQ :: bam2aln output
AACGGTGGGAGCGGGCGTGCCCGCGAAACAGGCGCCGCGGTGCATGGCCACGGCTTTGCCGGTGTT‑TCGGGCACG‑CCGCTCCCACAGACTGATTGCCATTAAGCGGGCCTATCGCTACAGTGACGGCCCGTTTTTTGTTGCCTCGCTAACGAATCATGACTCCCTTAGAACGCTATCAAGCAGATCTGAAACGTCCCGACTTCTTCCATGACGCGGCGC > NC_002947_CJ‑RC/1499432‑1499650
|
cgggggggggggggggggccccgaaaaccgggccggggggtgctgcccccgggtttggggggtggcggggcccccccCCGCTCCCACAGACTGATTGCCATTAAGCGGGCCTATCGCTACAGTGACGGCCCGTTTTTTGTTGCCTCGCTAA < NB501016:282:H2V7GAFX2:3:11604:16280:12288/74‑1 (MQ=60)
ggggggggggcggcgccgccccaccccgcggggcccgggcccccgcccggggtgggggggggcggggcccccccccCCGCTCCCACAGACTGATTGCCATTAAGCGGGCCTATCGCTACAGTGACGGCCCGTTTTTTGTTGCCTCGCTAAC < NB501016:282:H2V7GAFX2:2:21302:5469:16500/75‑1 (MQ=60)
gcggcgtgtgtccggcacaaaccccgggggggggttctcggtcccgggtttggggttttggccggcggccccCCGCTCCCACAGACTGATTGCAATTAAGCGGGCCTATCGCTACAGTGACGGCCCGTTTTTTGTTGCCTCGCTAACGAA < NB501016:282:H2V7GAFX2:4:21404:4897:9512/78‑1 (MQ=60)
gggggcgcccgcaaaaatcgcccgcggttcccggccccggggttctcggggtggcgcgtgacccgcCCGCTCCCACAGACTGATTGCCATTAAGCGGGCCTATCGCTACAGTGACGGCCCGTTTTTTGTTGCCTCGCTAACGAATCATGAC < NB501016:282:H2V7GAFX2:3:11602:3051:6115/85‑1 (MQ=60)
ccccccaaacccgggcgggggggcccgcccggggggtggggtggggggcggccccccccccCCGCTCCCACAGACTGATTGCCATTAAGCGGGCCTATCGCTACAGTGACGGCCCGTTTTTTGTTGCCTCGCTAACGAATCATGACTCCCT < NB501016:282:H2V7GAFX2:2:11312:3456:4344/90‑1 (MQ=60)
GCCCGCGAAACAGGCGCCGCGGTGCATGGCACCGGCTTTGCCGGTGTTCGCGGGCCCGCCCGCGCCCACAGACTGATTGCCATTAAGCGGGCCTATCGCTACAGTGACGGCCCGGTTTTTGTTGCCTCGCTTACGAATCATGACTGCCTTT > NB501016:282:H2V7GAFX2:1:21305:17530:3339/1‑151 (MQ=60)
CCCGCGAAACAGGCGCCGCGGTGCATGGCACCGGCTTTGCCGGTGTTCGCGGGCACGCCCGCTCCCACAGACTGATTGCCATTAAGCGGGCCTATCGCTACAGTGACGGCCCGTTTTTTGTTGCCTCGCTAACGAATCATGACTCCCTT > NB501016:282:H2V7GAFX2:1:21206:7334:3946/1‑149 (MQ=60)
CGCGAAACAGGCGCCGCGGTGCATGGCACCGGCTTTGCCGGTGTTCGCGGGCACGCCCGCTCCCACAGACTGATTGCCATTAAGCGGGCCTATCGCTACAGTGACGGCCCGTTTTTTGTTGCCTCGCTAACGAATCATGACTCCCTTAGA > NB501016:282:H2V7GAFX2:3:11601:13163:13931/1‑150 (MQ=60)
AGGCGCCGCGGTGCATGGCACCGGCTTTGCCGGTGTTCGCGGGCACGCCCGCTCCCACAGACTGATTGCCATTAAGCGGGCCTATCGCTACAGTGACGGCCCGTTTTTTGTTGCCTCGCTAACGAATCATGACTCCCTTAGAACGCTATC > NB501016:282:H2V7GAFX2:2:21109:2026:9012/1‑150 (MQ=60)
CATGGCACCGGCTTTGCCGGTGTTCGCGGGCACGCCCGCTCCCACAGACTGATTGCCATTAAGCGGGCCTATCGCTACAGTGACGGCCCGTTTTTTGTTGCCTCGCTAACGAATCATGACTCCCTTAGAACGCTATCAAGCAGATCTGAA > NB501016:282:H2V7GAFX2:3:21610:15902:17805/1‑150 (MQ=60)
TGGCACCGGCTTTGCCGGTGTTCGCGGGCACGCCCGCTCCCACAGACTGATTGCCATTAAGCGGGCCTATCGCTACAGTGACGGCCCGTTTTTTGTTGC < NB501016:282:H2V7GAFX2:2:11304:3822:12933/99‑1 (MQ=55)
acCGGCTTTGCCGGTGTTCGCGGGCACGCCCGCTCCCACAGACTGATTGCCATTAAGCCGGCCTATCGCTACAGTGACGGCCCGGTTTTTGTTGCCTCGCTAACGCAGCATGACTCCCTTAGAACGCTATCAAGGAGATCTGAAACGTCCC > NB501016:282:H2V7GAFX2:3:11411:20413:17220/3‑151 (MQ=60)
gtggtggggggtgggccgcccccccccCCGCTCCCACAGACTGATTGCCATTAAGCGGGCCTATCGCTACAGTGACGGCCCGTTTTTTGTTGCCTCGCTAACGAATCATGACTCCCTTAGAACGCTATCAAGCAGATCTGAAACGTCCCG < NB501016:282:H2V7GAFX2:1:11305:16697:8071/123‑1 (MQ=60)
gcggggtggggggcccccccccCCGCTCCCACAGACTGATTGCCATTAAGCGGGCCTATCGCTACAGTGACGGCCCGTTTTTTGTTGCCTCGCTAACGAATCATGACTCCCTTAGAACGCTATCAAGCAGATCTGAAACGTCCCGACTTC < NB501016:282:H2V7GAFX2:1:11110:18713:12836/128‑1 (MQ=60)
GCCGGTGTTCGCGGGCACGCCCGCTCCCACAGACTGATTGCCATTAAGCGGGCCTATCGCTACAGTGACGGCCCGTTTTTTGTTGCCTCGCTAACGAATCATGACTCCCTTAGCACGCTATCAAGCAGATCTGAAACGTCCCGACTTCTTC > NB501016:282:H2V7GAFX2:4:21412:13842:7796/1‑151 (MQ=60)
gggggcgccccccccccCCGCTCCCACAGACTGATTGCCATTAAGCGGGCCTATCGCTACAGTGACGGCCCGTTTTTTGTTGCCTCGCTAACGAATCATGACTCCCTTAGAACGCTATCAAGCAGATCTGAAACGTCCCGACTTCTTCCAT < NB501016:282:H2V7GAFX2:2:11210:12819:20050/134‑1 (MQ=60)
GGCACGCCCGCTCCCACAGACTGATTGCCATTAAGCGGGCCTATCGCTACAGTGACGGCCCGTTTTTTGTTGCCTCGCTAACGAATCATGACTCCCTTAGAACGCTATCAAGCAGATCTGAAACGTCCCGACTTCTTCCATGACGCGGCGC > NB501016:282:H2V7GAFX2:3:11411:13468:13403/1‑151 (MQ=60)
CACGCCCGCTCCCACAGACTGATTGCCATTAAGCGGGCCTATCGCTACAGTGACGGCCCGTTTTTTGTTGCCTCGCTAACGAATCATGACTCCCTTAGAACGCTATCAAGCAGATCTGAAACGTCCCGACTTCTTCCATGACGCGGCGC > NB501016:282:H2V7GAFX2:3:11611:4478:14710/1‑149 (MQ=60)
|
AACGGTGGGAGCGGGCGTGCCCGCGAAACAGGCGCCGCGGTGCATGGCCACGGCTTTGCCGGTGTT‑TCGGGCACG‑CCGCTCCCACAGACTGATTGCCATTAAGCGGGCCTATCGCTACAGTGACGGCCCGTTTTTTGTTGCCTCGCTAACGAATCATGACTCCCTTAGAACGCTATCAAGCAGATCTGAAACGTCCCGACTTCTTCCATGACGCGGCGC > NC_002947_CJ‑RC/1499432‑1499650
|
| Alignment Legend |
|---|
Aligned base mismatch/match (shaded by quality score): ATCG/ATCG < 0 ≤ ATCG/ATCG < 14 ≤ ATCG/ATCG < 15 ≤ ATCG/ATCG < 32 ≤ ATCG/ATCG < 36 ≤ ATCG/ATCG |
Unaligned base: atcg Masked matching base: atcg Alignment gap: ‑ Deleted base: ‑ |
