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 |
|
A2 F13 I1 R1
|
58 |
75.1 |
3211970 |
98.6% |
3167002 |
146.1 |
Breseq alignment
BRESEQ :: Evidence
|
| evidence |
seq id |
position |
mutation |
annotation |
gene |
description |
| RA |
NC_002947_CJ‑RC |
1,126,647 |
+C |
intergenic (‑101/+48) |
tdcG‑II ← / ← gcvP‑I |
L‑serine dehydratase/glycine dehydrogenase |
|
| |
seq id |
position |
ref |
new |
freq |
score (cons/poly) |
reads |
annotation |
genes |
product |
| * | NC_002947_CJ‑RC | 1,126,645 | 1 | . | C | 93.8%
| 50.8
/ ‑2.6
| 16 | intergenic (‑99/+50) | tdcG‑II/gcvP‑I | L‑serine dehydratase/glycine dehydrogenase |
| Reads supporting (aligned to +/- strand): ref base . (1/0); new base C (13/2); total (14/2) |
| Fisher's exact test for biased strand distribution p-value = 1.00e+00 |
| Kolmogorov-Smirnov test that lower quality scores support variant p-value = 9.28e-01 |
GAGGGGCCGATGCCGATCTTGAACAGGTCGAAGACGCTCAGTGACATGTGGACCTCCTGCCAGGTTGTTGGGTGGACATTGAGCCCTGTAGGCGCGGGTTTACCCGCGAATGCGGAGGTATAGCCACCATCGCATTCGCGGGT‑AAA‑CCGCTCCTACACAGAGCCCGCCACCCAAGCCAGGTGGCGGGGAGGGCTATCAGGCGTCCTGATAGCTCTCGATCGACGGGCAGGCGCACACCAGGTTGCGGTCGCCGAACACGTTGTCGACCCGGCCGACCGGCGGCCAG > NC_002947_CJ‑RC/1126500‑1126785
|
gAGGGGCCGATGCCGATCTTGAACAGGTCGAAGACGCTCAGTGACATGTGGACCTCCTGCCAGGTTGTTGGGTGGACATTGAGCCCTGTAGGCGCGGGTTTACCCGCGAATGCGGAGGTATAGCCACCATCGCATTCGCGGGT‑AAA‑c < 8:224673/147‑1 (MQ=255)
actggTCCAACACGCTCAGTCACATGTGCACCACCTGCCTGGTTGTTGGGTGCACATTGAGCCCTTTCGGCGGGGGTTACCCCGCTAATGGGTTGTTATACCCACCATCGCATTCGGGGTA‑AAACCCGCTCCTACACAGAGCCCGCCAc < 2:42554/146‑1 (MQ=255)
tttACCCGCGAATGCGGAGGTATAGCCACCATCGCATTCGCGGGT‑AAACCCGCTCCTACACAGAGCCCGCCCCCCAAGCCAGGTGGCGGGGAGGGCTATCAGGCGTCCTGATAGCTCTCGATCGACGGGCAGGCGCACACCAGGTTGCg > 2:320906/1‑149 (MQ=255)
ccagcgAATGCGGAGGTATAGCCACCATCGCAATCGCGGGTAAAA‑CAGCTCCTACACAGAGCCCGCCACCCACGCCAGCTGGCGGGGAGGGATATCAGGCTTCCGGATAGCTCTCGATCGACGGGCAGGCGCACACCAGGTTGCGGTCg > 8:355769/4‑149 (MQ=255)
ccGCGAATGCGGAGGTATAGCCACCATCGCATTCGCGGGT‑AAACCCGCTCCTACACAGAGCCCGCCACCCAAGCCAGGTGGCGGGGAGGGCTATCAGGCGTCCTGATAGCTCTCGATCGACGGGCAGGCGCACACCAGGTTGCGGTCGc > 3:195759/1‑149 (MQ=255)
cgcgAATGCGGAGGTATAGCCACCATCGCATTCGCGGGT‑AAACCCGCTCCTACACAGAGCCCGCCACCCAAGCCAGGTGGCGGGGAGGGCTATCAGGCGTCCTGATAGCTCTCGATCGACGGGCAGGCGCCCACCAGGTTGCGGTCGcc > 4:49826/1‑149 (MQ=255)
cgcgAATGCGGAGGTATAGCCACCATCGCATTCGCGGGT‑AAACCCGCTCCTACACAGAGCCCGCCACCCAAGCCAGGTGGCGGGGAGGGCTATCAGGCGTCCTGATAGCTCTCGATCGACGGGCAGGCGCACACCAGGTTGCGGTCGcc > 7:327033/1‑149 (MQ=255)
ggAGGTATAGCCACCATCGCATTCGCGGGT‑AAACCCGCTCCTACACAGAGCCCGCCACCCAAGCCAGGTGGCGGGGAGGGCTATCAGGCGTCCTGATAGCTCTCGATCGACGGGCAGGCGCACACCAGGTTGCGGTCGCCGAACACGtt > 5:122049/1‑149 (MQ=255)
ataGCCACCATCGCATTCGCGGGT‑AAACCCGCTCCTACACAGAGCCCGCCACCCAAGCCAGGTGGCGGGGAGGGCTATCAGGCGTCCTGATAGCTCTCGATCGACGGGCAGGCGCACACCAGGTTGCGGTCGCCGAACACGTTGTCGAc > 1:90472/1‑149 (MQ=255)
taGCCACCATCGCATTCGCGGGT‑AAACCCGCTCCTACACAGAGCCCGCCACCCAAGCCAGGTGGCGGGGAGGGCTATCAGGCGTCCTGATAGCTCTCGATCGACGGGCAGGCGCACACCAGGTTGCGGTCGCCGAACACGTTGTCGAcc > 2:378137/1‑149 (MQ=255)
cATTCGCGGGT‑AAACCCGCTCCTACACAGAGCCCGCCACCCAAGCCAGGTGGCGGGGAGGGCTATCAGGCGTCCTGATAGCTCTCGATCGACGGGCAGGCGCACACCAGGTTGCGGTCGCCGAACACGTTGTCGACCCGGCCGACcggc > 1:35242/1‑149 (MQ=255)
aTTCGCGGGT‑AAACCCGCTCCTACACAGAGCCCGCCACCCAAGCCAGGTGGCGGGGAGGGCTATCAGGCGTCCTGATAGCTCTCGATCGACGGGCAGGCGCACACCAGGTTGCGGTCGCCGAACACGTTGTCGACCCGGCCGACcggcg > 1:240957/1‑149 (MQ=255)
ttCGCGGGT‑AAACCCGCTCCTACACAGAGCCCGCCACCCAAGCCAGGTGGCGGGGAGGGCTATCAGGCGTCCTGATAGCTCTCGATCGACGGGCAGGCGCACACCAGGTTGCGGTCGCCGAACACGTTGTCGACCCGGCCGACcggcgg > 1:182273/1‑149 (MQ=255)
gcgGGT‑AAACCCGCTCCTACACAGAGCCCGCCACCCAAGCCAGGTGGCGGGGAGGGCTATCAGGCGTCCTGATAGCTCTCGATCGACGGGCAGGCGCACACCAGGTTGCGGTCGCCGAac < 2:277515/120‑1 (MQ=255)
gcgGGT‑AAACCCGCTCCTACACAGAGCCCGCCACCCAAGCCAGGTGGCGGGGAGGGCTATCAGGCGTCCTGATAGCTCTCGATCGACGGGCAGGCGCACACCAGGTTGCGGTCGCCGAac > 1:277515/1‑120 (MQ=255)
gcgGGT‑AAACCCGCTCCTACACAGAGCCCGCCACCCAAGCCAGGTGGCGGGGAGGGCTATCAGGCGTCCTGATAGCTCTCGATCGACGGGCAGGCGCACACCAGGTTGCGGTCGCCGAACACGTTGTCGACCCGGCCGCCCggcggc > 5:288561/1‑147 (MQ=255)
gggT‑AAACCCGCTCCTACACAGAGCCCGCCACCCAAGCCAGGTGGCGGGGAGGGCTATCAGGCGTCCTGATAGCTCTCGATCGACGGGCAGGCGCACACCAGGTTGCGGTCGCCGAACACGTTGTCGACCCGGCCGACCGGCGGCCAg > 1:339338/1‑148 (MQ=255)
|
GAGGGGCCGATGCCGATCTTGAACAGGTCGAAGACGCTCAGTGACATGTGGACCTCCTGCCAGGTTGTTGGGTGGACATTGAGCCCTGTAGGCGCGGGTTTACCCGCGAATGCGGAGGTATAGCCACCATCGCATTCGCGGGT‑AAA‑CCGCTCCTACACAGAGCCCGCCACCCAAGCCAGGTGGCGGGGAGGGCTATCAGGCGTCCTGATAGCTCTCGATCGACGGGCAGGCGCACACCAGGTTGCGGTCGCCGAACACGTTGTCGACCCGGCCGACCGGCGGCCAG > NC_002947_CJ‑RC/1126500‑1126785
|
| 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
TCGAAGACGCTCAGTGACATGTGGACCTCCTGCCAGGTTGTTGGGTGGACATTGAGCCCTGTAGGCGCGGGTTTACCCGCGAATGCGGAGGTATAGCCACCATCGCATTCGCGGGTAAA‑CCGCTCCTACACAGAGCCCGCCACCCAAGCCAGGTGGCGGGGAGGGCTATCAGGCGTCCTGATAGCTCTCGATCGACGGGCAGGCGCACACCAGGTTGCGGTCGCCGAACACGTTGTCGACCCGGCCGACCGGCGGCCAGTACTTGCCTTC > NC_002947_CJ‑RC/1126527‑1126796
|
gccaccccgcgcccagccctgcccccggcccccggggtggtggggccacctccgcccccgcccgcgcggggtacccccgctatggcgctgtaacccccccacccccttgcgggtaaaaccCCGCTCCTACACAGAGCCCGCCACCCAAGCC < NB501016:282:H2V7GAFX2:1:11112:7780:20152/31‑1 (MQ=60)
accccgccctgtcccttgggcccccccgccctggggtttgggggcaaatcccccccttgcgggggggtttaccccgctaagggggtgtaaacccccccagcccatgcggggtaaaacCCGCTCCTACACAGAGCCCGCCACCCAAGCCAGG < NB501016:282:H2V7GAFX2:3:11512:6343:4016/34‑1 (MQ=60)
gctccattgcttttgtccccccgggctgttggttggggtcttcgtcccgccctcgccggggggtttctcggggtgtgggcgttttatccgcccgaccctttggggcttaaacccCCGCTCCTACACAGAGCCCGCCACCCAAGCCAGGTGG < NB501016:282:H2V7GAFX2:1:11303:2056:13033/37‑1 (MQ=60)
ccccggcactggggcccgccgggcggggtgttggggggcacttgcccccgggggggccgggttcaccccgctatgggggcgcatccccccccacccctccgggggtaaaccCCGCTCCTACACAGAGCCCGCCACCCAAGCCAGGTGGCGG < NB501016:282:H2V7GAFX2:4:11612:3859:18732/40‑1 (MQ=60)
actttcctggcccccccccgccctggggttggggtgccacctgccccttgggggggggggcaccccccccatgggcgttcaacccccccccccccctgcgggttaaacccCCGCTCCTACACAGAGCCCGCCACCCAAGCCAGGTGGCGGG < NB501016:282:H2V7GAFX2:2:21307:23387:6663/41‑1 (MQ=60)
atcaaggcacacgcggggctgggttttctgcctctattaccccccctgcgggcgggtaaccccgcccacggcgttatacacccaaaacctaaacccctccaaaaccCCGCTCCTACACAGAGCCCGCCACCCAAGCCAGGTGGCGGGGAG < NB501016:282:H2V7GAFX2:3:11405:22256:3002/44‑1 (MQ=60)
gtggttgtggtttcatttcccccctttggggggttgtttccccggttattgcggttataaccccaccatcttctggggtttaaaccCCGCTCCTACACAGAGCCCGCCACCCAAGCCAGGTGGCGGGGAGGGCTATCAGGCGTCCTGATA < NB501016:282:H2V7GAFX2:4:21608:16148:12596/64‑1 (MQ=60)
gggtggtgggggcaaattgcccccgggcgggggggttccaccccgcatgggctccctaaccccccccccccccgccgggtaaacccCCGCTCCTACACAGAGCCCGCCACCCAAGCCAGGTGGCGGGGAGGGCTATCAGGCGTCCTGAT < NB501016:282:H2V7GAFX2:2:11111:13278:3620/63‑1 (MQ=60)
ggttttgggggttcatttccgccgttgcgggggggtttaccccgctattcgtttgaatccccacccctgctttggtgttaaacccCCGCTCCTACACAGAGCCCGCCACCCAAGCCAGGTGGCGGGGAGGGCTATCAGGCGTCCTGATAG < NB501016:282:H2V7GAFX2:4:11605:14561:1766/65‑1 (MQ=60)
ggtgttggggggcaatttgccccctgtgggggggggtacccccgctattggggctctatccccaccacccaatggggggtaaaccCCGCTCCTACACAGAGCCCGCCACCCAAGCCAGGTGGCGGGGAGGGCTATCAGGCGTCCTGATAGC < NB501016:282:H2V7GAFX2:3:11606:5189:9228/66‑1 (MQ=60)
tgggtgtcactttcccccggtgcgggggggtttacccgcttatggggttttaaacccccccacccattggggggtaaaccCCGCTCCTACACAGAGCCCGCCACCCAAGCCAGGTGGCGGGGAGGGCTATCAGGCGTCCTGATAGCTCTC < NB501016:282:H2V7GAFX2:2:11211:14672:12371/70‑1 (MQ=60)
cccgcgtgggggggggtctatcccccgctttggggttctaaccccccccctccctgggggttaaacccCCGCTCCTACACAGAGCCCGCCACCCAAGCCAGGTGGCGGGGAGGGCTATCAGGCGTCCTGATAGCTCTCGATCGACGGGCAG < NB501016:282:H2V7GAFX2:1:21208:5332:2699/83‑1 (MQ=60)
ggggtttcacccggttatggggtgtttacccccacatccccttggggttaaaaccCCGCTCCTACACAGAGCCCGCCACCCAAGCCAGGTGGCGGGGAGGGCTATCAGGCGTCCTGATAGCTCTCGATCGACGGGCAGGCGCACACCAGGT < NB501016:282:H2V7GAFX2:3:11502:4865:19659/96‑1 (MQ=60)
gggggttacccctgctactgcgttgttaacccacccagcgattgggggttaaaacCCGCTCCTACACAGAGCCCGCCACCCAAGCCAGGTGGCGGGGAGGGCTATCAGGCGTCCTGATAGCTCTCGATCGACGGGCAGGCGCACACCAGGT < NB501016:282:H2V7GAFX2:4:21609:7852:7290/96‑1 (MQ=60)
ttcccccgttatggggttgttaaccccacaacccattcggggttaaaccCCGCTCCTACACAGAGCCCGCCACCCAAGCCAGGTGGCGGGGAGGGCTATCAGGCGTCCTGATAGCTCTCGATCGACGGGCAGGCGCACACCAGGTTGCGG < NB501016:282:H2V7GAFX2:3:11404:7374:2520/101‑1 (MQ=60)
CCCGCGAATGCGGAGGTATAGCCACCATCGCATTCGCGGGTAAACCCGCTCCTACACAGAGCCCGCCACCCAAGCCAGGTGGCGGGGAGGGCTATCAGGCGTCCTGATAGCTCTCGATCGACGGGCAGGCGCACACCAGGTTGCGGTCGCC > NB501016:282:H2V7GAFX2:2:11311:21553:6813/1‑151 (MQ=60)
CCGCGAATGCGGAGGTATAGCCACCATCGCATTCGCGGGTAAACCCGCTCCTACACAGAGCCCGCCACCCAAGCCAGGTGGCGGGGAGGGCTATCAGGCGTCCTGATAGCTCTCGATCGACGGGCAGGCGCACACCAGGTTGCGGTCGCCG > NB501016:282:H2V7GAFX2:4:21509:24324:18984/1‑151 (MQ=60)
CGGAGGTATAGCCACCATCGCATTCGCGGGTAAACCCGCTCCTACACAGAGCCCGCCACCCAAGCCAGGTGGCGGGGAGGGCTATCAGGCGTCCTGATAGCTCTCGATCGACGGGCAGGCGCACACCAGGTTGCGGTCGCCGAACACGTTG > NB501016:282:H2V7GAFX2:3:11510:10482:19415/1‑151 (MQ=60)
caaaccaccctcatcgtctcggttcaaaaccCCGCTCCTACACAGAGCCCGCCACCCAAGCCAGGTGGCGGGGAGGGCTATCAGGCGTCCTGATAGCTCTCGATCGACGGGCAGGCGCACACCAGGTTGCGGTCGCCGAACACGTTGTCG < NB501016:282:H2V7GAFX2:2:21101:26440:3164/119‑1 (MQ=60)
TATAGCCACCATCGCATTCGCGGGTAAACCCGCTCCTACACAGAGCCCGCCACCCAAGCCAGGTGGCGGGGAGGGCTATCAGGCGTCCTGATAGCTCTCGATCGACGGGCAGGCGCACACCAGGTTGCGGTCGCCGAACACGTTGTCGACC > NB501016:282:H2V7GAFX2:1:11203:24090:18325/1‑151 (MQ=60)
GCATTCGCGGGTAAACCCGCTCCTACACAGAGCCCGCCACCCAAGCCAGGTGGCGGGGAGGGCTATCAGGCGTCCTGATAGCTCTCGATCGACGGGCAGGCGCACACCAGGTTGCGGTCGCCGAACACGTTGTCGACCCGGCCGACCGGCG > NB501016:282:H2V7GAFX2:1:11106:11494:14259/1‑151 (MQ=60)
CATTCGCGGGTAAACCCGCTCCTACACAGAGCCCGCCACCCAAGCCAGGTGGCGGGGAGGGCTATCAGGCGTCCTGATAGCTCTCGATCGACGGGCAGGCGCACACCAGGTTGCGGTCGCCGAACACGTTGTCGACCCGGCCGACCGGCGG > NB501016:282:H2V7GAFX2:1:21106:12996:10922/1‑151 (MQ=60)
ATTCGCGGGTAAACCCGCTCCTACACAGAGCCCGCCACCCAAGCCAGGTGGCGGGGAGGGCTATCAGGCGTCCTGATAGCTCTCGATCGACGGGCAGGCGCACACCAGGTTGCGGTCGCCGAACACGTTGTCGACCCGGCCGACCGGCGGG > NB501016:282:H2V7GAFX2:1:11308:9803:3015/1‑151 (MQ=60)
CGCGGGTAAACCCGCTCCTACACAGAGCCCGCCACCCAAGCCAGGTGGCGGGGAGGGCTATCAGGCGTCCTGATAGCTCTCGATCGACGGGCAGGCGCACACCAGGTTGCGGTCGCCGAACACGTTGTCGACCCGGCCGCCCGGCGGCC > NB501016:282:H2V7GAFX2:3:21504:25068:19616/1‑149 (MQ=60)
CGCGGGTAAACCCGCTCCTACACAGAGCCCGCCACCCAAGCCAGGTGGCGGGGAGGGCTATCAGGCGTCCTGATAGCTCTCGATCGACGGGCAGGCGCACACCAGGTTGCGGTCGCCGAACA > NB501016:282:H2V7GAFX2:1:21201:16701:5126/1‑122 (MQ=60)
gggttaaacCCGCTCCTACACAGAGCCCGCCACCCAAGCCAGGTGGCGGGGAGGGCTATCAGGCGTCCTGATAGCTCTCGATCGACGGGCAGGCGCACACCAGGTTGCGGTCGCCGAACACGTTGTCGACCCGGCCGACCGGCGGCCAGTA < NB501016:282:H2V7GAFX2:4:11511:3995:7060/142‑1 (MQ=60)
CGGGTAAACCCGCTCCTACACAGAGCCCGCCACCCAAGCCAGGTGGCGGGGAGGGCTATCAGGCGTCCTGATAGCTCTCGATCGACGGGCAGGCGCACACCAGGTTGCGGTCGCCGAACACGTTGTCGACCCGGCCGACCGGCGGCCAGT > NB501016:282:H2V7GAFX2:1:21212:9483:4556/1‑150 (MQ=60)
AAC‑CCGCTCCTACACAGAGCCCGCCACCCAAGCCAGGTGGCGGGGAGGGCTATCAGGCGTCCTGATAGCTCTCGATCGACGGGCAGGCGCACACCAGGTTGCGGTCGCCGAACACGTTGTCGACCCGGCCGACCGGCGGCCAGTACTTGCC > NB501016:282:H2V7GAFX2:4:11505:12249:3990/1‑151 (MQ=60)
CCGCTCCTACACAGAGCCCGCCACCCAAGCCAGGTGGCGGGGAGGGCTATCAGGCGTCCTGATAGCTCTCGATCGACGGGCAGGCGCACACCAGGTTGCGGTCGCCGAACACGTTGTCGACCCGGCCGACCGGCGGCCAGTACTTGCCTTC < NB501016:282:H2V7GAFX2:2:11110:11432:14626/151‑1 (MQ=60)
|
TCGAAGACGCTCAGTGACATGTGGACCTCCTGCCAGGTTGTTGGGTGGACATTGAGCCCTGTAGGCGCGGGTTTACCCGCGAATGCGGAGGTATAGCCACCATCGCATTCGCGGGTAAA‑CCGCTCCTACACAGAGCCCGCCACCCAAGCCAGGTGGCGGGGAGGGCTATCAGGCGTCCTGATAGCTCTCGATCGACGGGCAGGCGCACACCAGGTTGCGGTCGCCGAACACGTTGTCGACCCGGCCGACCGGCGGCCAGTACTTGCCTTC > NC_002947_CJ‑RC/1126527‑1126796
|
| Alignment Legend |
|---|
Aligned base mismatch/match (shaded by quality score): ATCG/ATCG < 0 ≤ ATCG/ATCG < 14 ≤ ATCG/ATCG < 15 ≤ ATCG/ATCG < 16 ≤ ATCG/ATCG < 36 ≤ ATCG/ATCG |
Unaligned base: atcg Masked matching base: atcg Alignment gap: ‑ Deleted base: ‑ |
