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 |
|
A1 F29 I1 R1
|
57 |
65.8 |
2790598 |
98.6% |
2751529 |
146.7 |
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 | 93.8%
| 48.1
/ ‑3.3
| 16 | intergenic (+83/‑81) | trpS/zapE | tryptophan‑‑tRNA ligase/nucleoside triphosphate hydrolase domain‑containing protein |
| Reads supporting (aligned to +/- strand): ref base . (0/1); new base C (11/4); total (11/5) |
| Fisher's exact test for biased strand distribution p-value = 3.12e-01 |
| Kolmogorov-Smirnov test that lower quality scores support variant p-value = 1.00e+00 |
AACGAAGCCTTGGCACCACAGCAGGACTGAGGCTGCCAAACGGTGGGAGCGGGCGTGCCCGCGAAACAGGCGCCGCGGTGCATGGCCACGGCTTTGCCGGTGTT‑TC‑‑GGGCACG‑C‑CGCTCCCACAGACTGATTGCCATTAAGCGGGCCTATCGCTACAGTGACGGCCCGTTTTTTGTTGCCTCGCTAACGAATCATGACTCCCTTAGAACGCTATCAAGCAGATCTGAAACGTCCCGACTTCTTCCATGACGCGGC > NC_002947_CJ‑RC/1499394‑1499648
|
aaCGAAGCGTTGCCACCACAGCTGGTCGTCGGCTGCAAAAGGGTGGGCGCGGGGGTGCCCGCTAAACCGGCGCGGCGGGGAATGCCACCGGCTTTGCGGGTGTTCGC‑‑GGCCACG‑CGCGCT‑CCACAGACTGATTGCCATTAAGCGGGc < 4:247414/147‑1 (MQ=255)
gcgggcggGCCCGCTAAACCGGCCCCGGGGCGCATGG‑CACCGGGTTGGCGGTGGT‑TCGGGGGCACGCC‑CGCTCCCACAGACTGATTGCCATTAAGCGGGCCTATCGCTACAGTGACGGCCCGTTTTTTGTTGCCTCGCTAACGAATCAt < 2:203460/149‑1 (MQ=255)
cccGCGAAACAGGCGCCGCGGTGCATGGCACCGGCTTTGCCGGTGTTCGC‑‑GGGCACGCC‑CGCTCCCACAGACTGATTGCCATTAAGCGGGCCTATCGCTACAGTGACGGCCCGTTTTTTGTTGCCTCGCTAACGAATCATGACTCCCt > 3:100926/1‑148 (MQ=37)
gcgAAACAGGCGCCGCGGTGCATGGCACCGGCTTTGCCGGTGTTCGC‑‑GGGCACGCC‑CGCTCCCACAGACTGATTGCCATTAAGCGGGCCTATCGCTACAGTGACGGCCCGTTTTTTGTTGCCTCGCTAACGAATCATGACTCCCTTAg > 8:181628/1‑148 (MQ=37)
aGGCGCCGCGGTGCATGGCACCGGCTTTGCCGGTGTTCGC‑‑GGGCACGCC‑CGCTCCCACAGACTGATTGCCATTAAGCGGGCCTATCGCTACAGTGACGGCCCGTTTTTTGTTGCCTCGCTAACGAATCATGACTCCCTTAGAACGCTAt > 2:51093/1‑149 (MQ=37)
ggCGCCGCGGTGCATGGCACCGGCTTTGCCGGTGTTCGC‑‑GGGCACGCC‑CGCTCCCACAGACTGATTGCCATTAAGCGGGCCTATCGCTACAGTGACGGCCCGTTTTTTGTTGCCTCGCTAACGAATCATGACTCCCTTAGAACGCTAt > 8:50793/1‑148 (MQ=37)
ggTGCATGGCACCGGCTTTGCCGGTGTTCGC‑‑GGGCACGCC‑CGCTCCCACAGACTGATTGCCATTAAGCGGGCCTATCGCTACAGTGACGGCCCGGTTTTTGTTGCCTCGCTAACGAATCATGACTCCCTTAGAACGCTATCAAg > 5:245414/1‑144 (MQ=37)
cGGCTTTGCCGGTGTTCGC‑‑GGGCACGCC‑CGCTCCCACAGACTGATTGCCATTAAGCGGGCCTATCGCTACAGTGACGGCCCGTTTTTTGTTGCCTCGCTAACGAATCATGACTCCCTTAGAACGCTATCAAGCAGATCTGAAACGTccc > 3:230088/1‑149 (MQ=39)
gCTTTGCCGGTGTTCGC‑‑GGGCACGCC‑CGCTCCCACAGACTGATTGCCATTAAGCGGGCCTATCGCTACAGTGACGGCCCGTTTTttgttg < 3:123343/90‑1 (MQ=25)
gCTTTGCCGGTGTTCGC‑‑GGGCACGCC‑CGCTCCCACAGACTGATTGCCATTAAGCGGGCCTATCGCTACAGTGACGGCCCGTTTTttgttg > 4:123343/1‑90 (MQ=25)
gCTTTGCCGGTGTTCGC‑‑GGGCACGCC‑CGCTCCCACAGACTGATTGCCATTAAGCGGGCCTATCGCTACAGTGACGGCCCGTTTTTTGTTGCCTCGCTAACGAATCATGACTCCCTTAGAACGCTATCAAGCAGATCTGAAACGTCCCGa > 3:191055/1‑149 (MQ=39)
tttGCCGGTGTTCGC‑‑GGGCACGCC‑CGCTCCCACAGACTGATTGCCATTAAGCGGGCCTATCGCTACAGTGACGGCCCGTTTTTTGTTGCCTCGCTAACGAATCATGACTCCCTTAGAACGCTATCAAGCAGATCTGAAACGTCCCGAct > 1:54684/1‑149 (MQ=39)
gc‑‑GGGCACGCC‑CGCTCCCACAGACTGATTGCCATTAAGCGGGCCTATCGCTACAGTGACGGCCCGTTTTTTGTTGCCTCGCTAACGAATCATGACTCCCTTAGAACGCTATCAAGCAGATCTGAAACGTCCCGACTTCTTCCATGAcgc > 5:213633/2‑149 (MQ=255)
gggCACGCC‑CGCTCCCACAGACTGATTGCCATTAAGCGGGCCTATCGCTACAGTGACGGCCCGTTTTTTGTTGCCTCGCTAACGAATCATGACTCCCTTAGAACGCTATc > 7:287240/1‑110 (MQ=255)
gggCACGCC‑CGCTCCCACAGACTGATTGCCATTAAGCGGGCCTATCGCTACAGTGACGGCCCGTTTTTTGTTGCCTCGCTAACGAATCATGACTCCCTTAGAACGCTATc < 8:287240/110‑1 (MQ=255)
ggCACGCC‑CGCTCCCACAGACTGATTGCCATTAAGCGGGCCTATCGCTACAGTGACGGCCCGTTTTTTGTTGCCTCGCTAACGAATCATGACTCCCTTAGAACGCTATCAAGCAGATCTGAAACGTCCCGACTTCTTCCATGACgcggc < 1:51093/149‑1 (MQ=255)
|
AACGAAGCCTTGGCACCACAGCAGGACTGAGGCTGCCAAACGGTGGGAGCGGGCGTGCCCGCGAAACAGGCGCCGCGGTGCATGGCCACGGCTTTGCCGGTGTT‑TC‑‑GGGCACG‑C‑CGCTCCCACAGACTGATTGCCATTAAGCGGGCCTATCGCTACAGTGACGGCCCGTTTTTTGTTGCCTCGCTAACGAATCATGACTCCCTTAGAACGCTATCAAGCAGATCTGAAACGTCCCGACTTCTTCCATGACGCGGC > NC_002947_CJ‑RC/1499394‑1499648
|
| Alignment Legend |
|---|
Aligned base mismatch/match (shaded by quality score): ATCG/ATCG < 3 ≤ ATCG/ATCG < 14 ≤ ATCG/ATCG < 15 ≤ ATCG/ATCG < 36 ≤ ATCG/ATCG |
Unaligned base: atcg Masked matching base: atcg Alignment gap: ‑ Deleted base: ‑ |
GATK/CNVnator alignment
BRESEQ :: bam2aln output
CTGAACGAAGCCTTGGCACCACAGCAGGACTGAGGCTGCCAAACGGTGGGAGCGGGCGTGCCCGCGAAACAGGCGCCGCGGTGCATGGCCACGGCTTTGCCGGTGTT‑TCGGGCACG‑CCGCTCCCACAGACTGATTGCCATTAAGCGGGCCTATCGCTACAGTGACGGCCCGTTTTTTGTTGCCTCGCTAACGAATCATGACTCCCTTAGAACGCTATCAAGCAGATCTGAAACGTCCCGACTTCTTCCATGACGCGGCGCAGG > NC_002947_CJ‑RC/1499391‑1499653
|
acacccgccggccgcacacccccgcgcggcgcggctgcatacggtggggggggggcgcccgcctacaccgcgggcgcgggtgaccggcgcggtttggggggtgttggggccgccccccCCGCTCCCACAGACTGATTGCCATTAAGCGGG < NB501016:282:H2V7GAFX2:1:11110:7989:19165/32‑1 (MQ=60)
cgcggcgggcccccccccgccgtgggggggccccacgggggggggggggggggccccctaaacggggggcggggggttcggcgccggggtgggggggggggggccgcccccccCCGCTCCCACAGACTGATTGCCATTAAGCGGGCCTATC < NB501016:282:H2V7GAFX2:4:11404:19286:10543/38‑1 (MQ=60)
gccggggggcccccacggggggggggggggggcccccccaaaccccgccggggggggccggcccggggggggggggggggggggggcccccccCCGCTCCCACAGACTGATTGCCATTAAGCGGGCCTATCGCTACAGTGACGGCCCGTTT < NB501016:282:H2V7GAFX2:1:11107:7404:8494/58‑1 (MQ=60)
ggggcgcccccccggggggggggggggggccccccccacccgggccgcggggggtcgggcccggggtgggggggggggggggcccccccccCCGCTCCCACAGACTGATTGCCATTAAGCGGGCCTATCGCTACAGTGACGGCCCGTTTTT < NB501016:282:H2V7GAFX2:2:11305:22001:5441/60‑1 (MQ=60)
ccccccccccggggggggggggggcccccccacaccccggcccgggggccgccgccccggggggggggggggggggggccccccccCCGCTCCCACAGACTGATTGCCATTAAGCGGGCCTATCGCTACAGTGACGGCCCGTTTTTTGTTG < NB501016:282:H2V7GAFX2:1:21211:7484:5675/65‑1 (MQ=60)
ggcggggggcgcccccccaaacccgggcgcggggcccccccccggggggggggggggggcgggcccccccccCCGCTCCCACAGACTGATTGCCATTAAGCGGGCCTATCGCTACAGTGACGGCCCGTTTTTTGTTGCCTCGCTAACGAAT < NB501016:282:H2V7GAFX2:4:21503:9584:10986/79‑1 (MQ=60)
GCCCGCGAAACAGGCGCCGCGGTGCATGGCACCGGCTTTGCCGGTGTTCGCGGGCACGCCCGCTCCCACAGACTGATTGCCATTAAGCGGGCCTATCGCTACAGTGACGGCCCGTTTTTTGTTGCCTCGCTAACGAATCATGACTCCCTT > NB501016:282:H2V7GAFX2:2:11210:14549:1601/1‑150 (MQ=60)
CGCGAAACAGGCGCCGCGGTGCATGGCACCGGCTTTGCCGGTGTTCGCGGGCACGCCCGCTCCCACAGACTGATTGCCATTAAGCGGGCCAAAAGCTACAGTGACGGCCCGGTTTTTGTTGGCTCGCTAACGAATCATGACTCCCGTAGA > NB501016:282:H2V7GAFX2:1:11311:20713:9010/1‑150 (MQ=60)
ggggtttcggcgggggtgtggggggttgtggggggcccccccCCGCTCCCACAGACTGATTGCCATTAAGCGGGCCTATCGCTACAGTGACGGCCCGTTTTTTGTTGCCTCGCTAACGAATCATGACTCCCTTAGAACGCTATCAAGCAGA < NB501016:282:H2V7GAFX2:2:21112:10990:15121/109‑1 (MQ=60)
CGGTGCATGGCACCGGCTTTGCCGGTGTTCGCGGGCACGCCCGCTCCCACAGACTGATTGCCATTAAGCGGGCCTATCGCTACAGTGACGGCCCGGTTTTTGTTGCCTCGCTAACGAATCATGACTCCCTTAGAACGCTATCAAGC > NB501016:282:H2V7GAFX2:3:21503:4031:6749/1‑146 (MQ=60)
ttcggccggggttttgggggttgggggggccccgccCCGCTCCCACAGACTGATTGCCATTAAGCGGGCCTATCGCTACAGTGACGGCCCGTTTTTTGTTGCCTCGCTAACGAATCATGACTCCCTTAGAACGCTATCAAGCAGATCTGA < NB501016:282:H2V7GAFX2:1:21101:21641:14736/114‑1 (MQ=60)
gtgtgttggggggggggggcggcccccccccCCGCTCCCACAGACTGATTGCCATTAAGCGGGCCTATCGCTACAGTGACGGCCCGTTTTTTGTTGCCTCGCTAACGAATCATGACTCCCTTAGAACGCTATCAAGCAGATCTGAAACGTC < NB501016:282:H2V7GAFX2:2:21104:1719:12027/120‑1 (MQ=60)
CCGGCTTTGCCGGTGTTCGCGGGCACGCCCGCTCCCACAGACTGATTGCCATTAAGCGGGCCTATCGCTACAGTGACGGCCCGTTTTTTGTTGCCTCGCTAACGAATCATGACTCCCTTAGAACGCTATCAAGCAGATCTGAAACGTCCCC > NB501016:282:H2V7GAFX2:2:21201:15272:3478/1‑151 (MQ=60)
GGCTTTGCCGGTGTTCGCGGGCACGCCCGCTCCCACAGACTGATTGCCATTAAGCGGGCCTATCGCTACAGTGACGGCCCGTTTTTTGTTGCCTCGCTAACGAATCATGACTCCCTTAGAACGCTATCAAGCAGATCTGAAACGTCCCGAC > NB501016:282:H2V7GAFX2:2:21104:1619:5742/1‑151 (MQ=60)
GGCTTTGCCGGTGTTCGCGGGCACGCCCGCTCCCACAGACTGATTGCCATTAAGCGGGCCTATCGCTACAGTGACGGCCCGTTTTTTGTTGC < NB501016:282:H2V7GAFX2:2:11302:15330:12334/92‑1 (MQ=60)
CTTTGCCGGTGTTCGCGGGCACGCCCGCTCCCACAGACTGATTGCCATTAAGCGGGCCTATCGCTACAGTGACGGCCCGTTTTTTGTTGCCTCGCTAACGAATCATGACTCCCTTAGAACGCTATCAAGCAGATCTGAAACGTCCCGACTT > NB501016:282:H2V7GAFX2:1:11111:6108:9363/1‑151 (MQ=60)
CCGGTGTTCGCGGGCACGCCCGCTCCCACAGACTGATTGCCATTAAGCGGGCCTATCGCTACAGTGACGGCCCGTTTTTTGTTGCCTCGCTAACGAATCATGACACCCTTAGAACGCTATCAAGCAGCTCTGAAACGTCCCGACTTCTTAC > NB501016:282:H2V7GAFX2:3:21402:20645:1986/1‑151 (MQ=60)
cgCGGGCACGCCCGCTCCCACAGACTGATTGCCATTAAGCGGGCCTATCGCTACAGTGACGGCCCGTTTTTTGTTGCCTCGCTAACGAATCATGACTCCCTTAGAACGCTATCAAGCAGATCTGAAACGTCCCGACTTCTTCCATGACGCG > NB501016:282:H2V7GAFX2:3:21408:22492:11583/3‑151 (MQ=60)
CGGGCACGCCCGCTCCCACAGACTGATTGCCATTAAGCGGGCCTATCGCTACAGTGACGGCCCGTTTTTTGTTGCCTCGCTAACGAATCATGACTCCCTTAGAACGCTATCA > NB501016:282:H2V7GAFX2:4:21510:7475:6392/1‑112 (MQ=60)
GGGCACGCCCGCTCCCACAGACTGATTGCCATTAAGCGGGCCTATCGCTACAGTGACGGCCCGTTTTTTGTTGCCTCGCTAACGAATCATGACTCCCTTAGAACGCTATCAAGCAGATCTGAAACGTCCCGACTTCTTCCATGACGCGGCG < NB501016:282:H2V7GAFX2:1:11110:15675:15076/151‑1 (MQ=60)
cgcCCGCTCCCACAGACTGATTGCCATTAAGCGGGCCTATCGCTACAGTGACGGCCCGTTTTTTGTTGCCTCGCTAACGAATCATGACTCCCTTAGAACGCTATCAAGCAGATCTGAAACGTCCCGACTTCTTCCATGACGCGGCGCAGG > NB501016:282:H2V7GAFX2:2:21301:15884:6497/4‑150 (MQ=60)
|
CTGAACGAAGCCTTGGCACCACAGCAGGACTGAGGCTGCCAAACGGTGGGAGCGGGCGTGCCCGCGAAACAGGCGCCGCGGTGCATGGCCACGGCTTTGCCGGTGTT‑TCGGGCACG‑CCGCTCCCACAGACTGATTGCCATTAAGCGGGCCTATCGCTACAGTGACGGCCCGTTTTTTGTTGCCTCGCTAACGAATCATGACTCCCTTAGAACGCTATCAAGCAGATCTGAAACGTCCCGACTTCTTCCATGACGCGGCGCAGG > NC_002947_CJ‑RC/1499391‑1499653
|
| Alignment Legend |
|---|
Aligned base mismatch/match (shaded by quality score): ATCG/ATCG < 0 ≤ 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: ‑ |
