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 F11 I1 R1
|
56 |
91.5 |
3907174 |
98.4% |
3844659 |
146.2 |
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 | 94.7%
| 60.9
/ ‑3.3
| 19 | intergenic (‑99/+50) | tdcG‑II/gcvP‑I | L‑serine dehydratase/glycine dehydrogenase |
| Reads supporting (aligned to +/- strand): ref base . (0/1); new base C (13/5); total (13/6) |
| Fisher's exact test for biased strand distribution p-value = 3.16e-01 |
| Kolmogorov-Smirnov test that lower quality scores support variant p-value = 1.00e+00 |
GGGCCGATGCCGATCTTGAACAGGTCGAAGACGCTCAGTGACATGTGGACCTCCTGCCAGGTTGTTGGGTGGACATTGAGCCCTGTAGGCGCGGGTTTACCCGCGAATGCGGAGGTATAGCCACCATCGCATTCGCGGGTAA‑A‑CCGCTCCTACACAGAGCCCGCCACCCAAGCCAGGTGGCGGGGAGGGCTATCAGGCGTCCTGATAGCTCTCGATCGACGGGCAGGCGCACACCAGGTTGCGGTCGCCGAACACGTTGTCGACCCGGCCGACCGGCG > NC_002947_CJ‑RC/1126503‑1126780
|
gggCCGATGCCGATCTTGAACAGGTCGAAGACGCTCAGTGACATGTGGACCTCCTGCCTGGTTGTTGGGTGGACATTGAGCCCTGTAGGCGCGGGTTTACCCGCGAATGCGGAGGTATAGCCACCATCGCATTCGCGGGTAA‑A‑cccgc < 8:389548/148‑4 (MQ=255)
acaCGCTAAGTTACTTGGGGACCACCTGCCTGGTTGTTGGGTGCAAATTGAGCCCTTTCGGGGGGGTTTAACCCGCTAATGGGTTGTTATACCCACAATCGAATTGGGGGTAAA‑ACCCGCTCCTACACAGAGCCCGCCACCCAAGCCa < 6:414223/146‑1 (MQ=255)
aCATGTGCACCTCCTGCCAGGTTGTTGGGTGCACTTTGAGCCCTGTAGGCGCGGGTTTACCCGCGAATGCGGAGGTATAGCCACCATCGCATTCGCGGTTAA‑ACCCGCTCCTACACAGAGCCCGCCACCCAAGCCAGGTGGCGGGGAg < 2:86785/148‑1 (MQ=38)
gcgGGTTTACCCGCGAATGCGGAGGTATAGCCACCATCGCATTCGCGGGTAA‑ACCCGCTCCTACACAGAGCCCGCCACCCAAGCCAGGTGGCGGGGAGGGCTATCAGGCGTCCTGATAGCTCTCGATCGACGGGCAGGCGCACACCAgg > 1:398197/1‑149 (MQ=255)
gcgGGTTTACCCGCGAATGCGGAGGTATAGCCACCATCGCATTCGCGGGTAA‑ACCCGCTCCTACACAGAGCCCGCCACCCAAGCCAGGTGGCGGGGAGGGCTATCAGGCGTCCTGATAGCTCTCGATCGACGGGCAGGCGCACACCAgg > 7:278023/1‑149 (MQ=255)
gTTTACCCGCGAATGCGGAGGTATAGCCACCATCGCATTCGCGGGTAA‑ACCCGCTCCTACACAGAGCCCGCCCCCCAAGCCAGGTGGCGGGGAGGGCTATCAGGCGTCCTGATAGCTCTCGATCGCCGGGCAGGCGCACACCAGGTTg > 5:382241/1‑148 (MQ=255)
tACCCGCGAATGCGGAGGTATAGCCACCATCGCATTCGCGGGTAA‑ACCCGCTCCTACACAGAGCCCGCCACCCAAGCCAGGTGGCGGGGAGGGCTATCAGGCGTCCTGATAGCTCTCGATCGACGGGCAGGCGCACCCCAAGTTGCGGt > 1:76011/1‑149 (MQ=255)
ccGCGAATGCGGAGGTATAGCCACCATCGCATTCGCGGGTAA‑ACCCGCTCCTACACAGAGCCCGCCACCCAAGCCAGGTGGCGGGGAGGGCTATCAGGCGTCCTGATAGCTCTCGATCGACGGGCAGGCGCACACCAGGTTGCGGTCGc > 4:299293/1‑149 (MQ=255)
ccGCGAATGCGGAGGTATAGCCACCATCGCATTCGCGGGTAA‑ACCCGCTCCTACACAGAGCCCGCCACCCAAGCCAGGTGGCGGGGAGGGCTATCAGGCGTCCTGATAGCTCTCGATCGACGGGCAGGCGCACACCAGGTTGCGGTCGc > 7:382652/1‑149 (MQ=255)
gcgAATGCGGAGGTATAGCCACCATCGCATTCGCGGGTAA‑ACCCGCTCCTACACAGAGCCCGCCACCCAAGCCAGGTGGCGGGGAGGGCTATCAGGCGTCCTGATAGCTCTCGATCGACGGGCAGGCGCACACCAGGTTGCGGTCGcc > 8:404012/1‑148 (MQ=255)
ggAGGTATAGCCACCATCGCATTCGCGGGTAA‑ACCCGCTCCTACACAGAGCCCGCCACCCAAGCCAGGTGGCGGGGAGGGCTATCAGGCGTCCTGATAGCTCTCGATCGACGGGCAGGCGCACACCAGGTTGCGGTCGCCGAACACGtt > 1:126012/1‑149 (MQ=255)
tttgTATACCCACCATCCCTTTCGCGGTTAACC‑CCGCTCCTACACAGAGCCCGCCACCCAAGCCAGGTGGCGGGGAGGGCTATCAGGCGTCCTGATAGCTCTCGATCGACGGGCAGGCGCACACCAGGTTGCGGTCGCCGAACACGtt < 6:449884/145‑1 (MQ=255)
taGCCACCATCGCATTCGCGGGTAA‑ACCCGCTCCTACACAGAGCCCGCCACCCAAGCCAGGTGGCGGGGAGGGCTATCAGGCGTCCTGATAGCTCTCGATCGACGGGCAGGCGCACACCAGGTTGCGGTCGCCGAACACGTTGTCGAcc > 1:286525/1‑149 (MQ=255)
taGCCACCATCGCATTCGCGGGTAA‑ACCCGCTCCTACACAGAGCCCGCCACCCAAGCCAGGTGGCGGGGAGGGCTATCAGGCGTCCTGATAGCTCTCGATCGACGGGCAGGCGCACACCAGGTTGCGGTCGCCGAACACGTTGTCGAc > 5:266031/1‑148 (MQ=255)
gCCACCATCGCATTCGCGGGTAA‑ACCCGCTCCTACACAGAGCCCGCCACCCAAGCCAGGTGGCGGGGAGGGCTATCAGGCGTCCTGATAGCTCTCGATCGACGGGCAGGCGCACACCAGGt > 6:133629/1‑121 (MQ=255)
ccaccaTCGCATTCGCGGGTAA‑ACCCGCTCCTACACAGAGCCCGCCACCCAAGCCAGGTGGCGGGGAGGGCTATCAg < 7:191699/77‑1 (MQ=255)
ccaccaTCGCATTCGCGGGTAA‑ACCCGCTCCTACACAGAGCCCGCCACCCAAGCCAGGTGGCGGGGAGGGCTATCAg > 8:191699/1‑77 (MQ=255)
ccaccaTCGCATTCGCGGGTAA‑ACCCGCTCCTACACAGAGCCCGCCACCCAAGCCAGGTGGCGGGGAGGGCTATCAGGCGTCCTGATAGCTCTCGATCGACGGGCAGGCGCACACCAGGtt < 5:133629/121‑1 (MQ=255)
gCATTCGCGGGTAA‑ACCCGCTCCTACACAGAGCCCGCCACCCAAGCCAGGTGGCGGGGAGGGCTATCAGGCGTCCTGATAGCTCTCGATCGACGGGCAGGCGCACACCAGGTTGCGGTCGCCGAACACGTTGTCGACCCGGctcaggtg > 8:242973/1‑142 (MQ=255)
ttCGCGGGTAA‑ACCCGCTCCTACACAGAGCCCGCCACCCAAGCCAGGTGGCGGGGAGGGCTATCAGGCGTCCTGATAGCTCTCGATCGACGGGCAGGCGCACACCAGGTTGCGGTCGCCGAACACGTTGTCGACCCGGCCGACcggcg < 6:266031/148‑1 (MQ=255)
|
GGGCCGATGCCGATCTTGAACAGGTCGAAGACGCTCAGTGACATGTGGACCTCCTGCCAGGTTGTTGGGTGGACATTGAGCCCTGTAGGCGCGGGTTTACCCGCGAATGCGGAGGTATAGCCACCATCGCATTCGCGGGTAA‑A‑CCGCTCCTACACAGAGCCCGCCACCCAAGCCAGGTGGCGGGGAGGGCTATCAGGCGTCCTGATAGCTCTCGATCGACGGGCAGGCGCACACCAGGTTGCGGTCGCCGAACACGTTGTCGACCCGGCCGACCGGCG > NC_002947_CJ‑RC/1126503‑1126780
|
| 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
GAAGACGCTCAGTGACATGTGGACCTCCTGCCAGGTTGTTGGGTGGACATTGAGCCCTGTAGGCGCGGGTTTACCCGCGAATGCGGAGGTATAGCCACCATCGCATTCGCGGGTAAA‑CCGCTCCTACACAGAGCCCGCCACCCAAGCCAGGTGGCGGGGAGGGCTATCAGGCGTCCTGATAGCTCTCGATCGACGGGCAGGCGCACACCAGGTTGCGGTCGCCGAACACGTTGTCGACCCGGCCGACCGGCGGCCAGTACTTGCC > NC_002947_CJ‑RC/1126529‑1126793
|
cacccccccctttcacttggccccccccgcccggttttttggttgcaattcaccccctgtggggggggttaaccccgcaatggcgtcgtaaacccccccccccaatgcgggttaaaccCCGCTCCTACACAGAGCCCGCCACCCAAGCCAG < NB501016:282:H2V7GAFX2:4:21509:1360:7785/33‑1 (MQ=60)
gcccctggggccccccccccgtggtttggggggtcacttcgcccggtgggggggggggttcccccgctatggggtcgctacccccaccacccctggggggtaaaaccCCGCTCCTACACAGAGCCCGCCACCCAAGCCAGGTGGCGGGG < NB501016:282:H2V7GAFX2:1:11211:9490:7097/42‑1 (MQ=60)
ccctgggccccccccgccgtgggtggggtgcgcactgcccgccggctcgggggggtcccccccgtactggcggcgaaaaccccccaccgacggggggtaaacccCCGCTCCTACACAGAGCCCGCCACCCAAGCCAGGTGGCGGGGAGGGC < NB501016:282:H2V7GAFX2:2:11307:17160:12185/47‑1 (MQ=60)
gcccggcggggttgtggggggggccccatggccccggtcggggggggtcccccccgggtcgggcgtttaaacccccccaccgccggggggtttaacccCCGCTCCTACACAGAGCCCGCCACCCAAGCCAGGTGGCGGGGAGGGCTATCAG < NB501016:282:H2V7GAFX2:3:21412:2371:12527/53‑1 (MQ=60)
ggggggggtccattgccccgtgtggggggggttaccccggcttggcggtttctaaccccccctccaattgggggtaaaaccCCGCTCCTACACAGAGCCCGCCACCCAAGCCAGGTGGCGGGGAGGGCTATCAGGCGTCCTGATAGCTCT < NB501016:282:H2V7GAFX2:1:21209:20047:13840/69‑1 (MQ=60)
ggggggttacccggttatggggttttaagcccccctagcccttcggggttaaaccCCGCTCCTACACAGAGCCCGCCACCCAAGCCAGGTGGCGGGGAGGGCTATCAGGCGTCCTGATAGCTCTCGATCGACGGGCAGGCGCACACCAGGT < NB501016:282:H2V7GAFX2:3:11502:11134:15742/96‑1 (MQ=60)
CGCGGGTTTACCCGCGAATGCGGAGGTATAGCCACCATCGCATTCGCGGGTAAACCCGCTCCTACACAGAGCCCGCCACCCAAGCCAGGTGGCGGGGAGGGCTATCAGGCGTCCTGATAGCTCTCGATCGACGGGCAGGCGCACACCAGGT > NB501016:282:H2V7GAFX2:1:21210:21922:18643/1‑151 (MQ=60)
CGCGGGTTTACCCGCGAATGCGGAGGTATAGCCACCATCGCATTCGCGGGTAAACCCGCTCCTACACAGAGCCCGCCACCCAAGCCAGGTGGCGGGGAGGGCTATCAGGCGTCCTGATAGCTCTCGATCGACGGGCAGGCGCACACCAGGT > NB501016:282:H2V7GAFX2:4:21404:9727:12352/1‑151 (MQ=60)
gggtttcccccgctattgggttggtaacgcacccaccgatttcgcgttaaaacCCGCTCCTACACAGAGCCCGCCACCCAAGCCAGGTGGCGGGGAGGGCTATCAGGCGTCCTGATAGCTCTCGATCGACGGGCAGGCGCACACCAGGTTG < NB501016:282:H2V7GAFX2:3:11506:21198:5456/98‑1 (MQ=60)
GGTTTACCCGCGAATGCGGAGGTATAGCCACCATCGCATTCGCGGGTAAACCCGCTCCTACACAGAGCCCGCCCCCCAAGCCAGGTGGCGGGGAGGGCTATCAGGCGTCCTGATAGCTCTCGATCGCCGGGCAGGCGCACACCAGGTTGCG > NB501016:282:H2V7GAFX2:3:21509:7901:7439/1‑151 (MQ=60)
TTACCCGCGAATGCGGAGGTATAGCCACCATCGCATTCGCGGGTAAACCCGCTCCTACACAGAGCCCGCCACCCAAGCCAGGTGGCGGGGAGGGCTATCAGGCGTCCTGATAGCTCTCGATCGACGGGCAGGCGCACCCCAAGTTGCGGTC > NB501016:282:H2V7GAFX2:1:11111:23686:9574/1‑151 (MQ=60)
CCCGCGAATGCGGAGGTATAGCCACCATCGCATTCGCGGGTAAACCCGCTCCTACACAGAGCCCGCCACCCAAGCCAGGTGGCGGGGAGGGCTATCAGGCGTCCTGATAGCTCTCGATCGACGGGCAGGCGCACACCAGGTTGCGGTCGCC > NB501016:282:H2V7GAFX2:4:21507:2833:6045/1‑151 (MQ=60)
ggtgttgtggggttttaccccccctatggcttgggggtttaaccCCGCTCCTACACTGAGCCCGCCACCCAAGCCAGGTGGCGGGGAGGGCTATCAGGCGTCCTGATAGCTCTCGATCGACGGGCAGGCGCACACCAGGTTGCGGTCGCCG < NB501016:282:H2V7GAFX2:3:11507:3494:12574/107‑1 (MQ=60)
ccgctatggggtttttaaccccacccgcccttgcgggttaaaccCCGCTCCTACACAGAGCCCGCCACCCAAGCCAGGTGGCGGGGAGGGCTATCAGGCGTCCTGATAGCTCTCGATCGACGGGCAGGCGCACACCAGGTTGCGGTCGCCG < NB501016:282:H2V7GAFX2:4:21609:17495:15747/107‑1 (MQ=60)
CGCGAATGCGGAGGTATAGCCACCATCGCATTCGCGGGTAAA‑CC > NB501016:282:H2V7GAFX2:4:11501:17522:16663/1‑44 (MQ=60)
CGGAGGTATAGCCACCATCGCATTCGCGGGTAAACCCGCTCCTACACAGAGCCCGCCACCCAAGCCAGGTGGCGGGGAGGGCTATCAGGCGTCCTGATAGCTCTCGATCGACGGGCAGGCGCACACCAGGTTGCGGTCGCCGAACACGTTG > NB501016:282:H2V7GAFX2:1:11206:6812:12990/1‑151 (MQ=60)
gatggtggctatacctcCGCATTCGCGGGTAAACCCGCTCCTACACAGAGCCCGCCACCCAAGCCAGGTGGCGGGGAGGGCTATCAGGCGTCCTGATAGCTCTCGATCGACGGGCAGGCGCACACCAGGTTGCGGTCGCCGAACACGTTGT < NB501016:282:H2V7GAFX2:1:21306:15468:8251/134‑1 (MQ=60)
ATAGCCACCATCGCATTCGCGGGTAAACCCGCTCCTACACAGAGCCCGCCACCCAAGCCAGGTGGCGGGGAGGGCTATCAGGCGTCCTGATAGCTCTCGATCGACGGGCAGGCGCACACCAGGTTGCGGTCGCCGAACACGTTGTCGACCC > NB501016:282:H2V7GAFX2:3:21403:5356:11062/1‑151 (MQ=60)
ATAGCCACCATCGCATTCGCGGGTAAACCCGCTCCTACACAGAGCCCGCCACCCAAGCCAGGTGGCGGGGAGGGCTATCAGGCGTCCTGATAGCTCTCGATCGACGGGCAGGCGCACACCAGGTTGCGGTCGCCGAACACGTTGTCGACCC > NB501016:282:H2V7GAFX2:1:21106:21894:5934/1‑151 (MQ=60)
AGCCACCATCGCATTCGCGGGTAAACCCGCTCCTACACAGAGCCCGCCACCCAAGCCAGGTGGCGGGGAGGGCTATCAGGCGTCCTGATAGCTCTCGATCGACGGGCAGGCGCACACCAGGTTG < NB501016:282:H2V7GAFX2:3:11508:18303:12479/124‑1 (MQ=60)
GCCACCATCGCATTCGCGGGTAAACCCGCTCCTACACAGAGCCCGCCACCCAAGCCAGGTGGCGGGGAGGGCTATCAGG < NB501016:282:H2V7GAFX2:4:11603:25163:20227/79‑1 (MQ=60)
gggcggtaaaacCCGCTCCTACACAGAGCCCGCCACCCAAGCCAGGTGGCGGGGAGGGCTATCAGGCGTCCTGATAGCTCTCGATCGACGGGCAGGCGCACACCAGGTTGCGGTCGCCGAACACGTTGTCGACCCGGCCGACCGGCGGCC < NB501016:282:H2V7GAFX2:4:11506:25725:13792/138‑1 (MQ=60)
ggtttaaacCCGCTCCTACACAGAGCCCGCCACCCAAGCCAGGTGGCGGGGAGGGCTATCAGGCGTCCTGATAGCTCTCGATCGACGGGCAGGCGCACACCAGGTTGCGGTCGCCGAACACGTTGTCGACCCGGCCGACCGGCGGCCAGTA < NB501016:282:H2V7GAFX2:4:21511:11942:20080/142‑1 (MQ=60)
cccCCGCTCCTACACAGAGCCCGCCACCCAAGCCAGGTGGCGGGGAGGGCTATCAGGCGTCCTGATAGCTCTCGATCGACGGGCAGGCGCACACCAGGTTGCGGTCGCCGAACACGTTGTCGACCCGGCCGACCGGCGGCCAGTACTTGCC < NB501016:282:H2V7GAFX2:1:21212:5510:2972/148‑1 (MQ=60)
|
GAAGACGCTCAGTGACATGTGGACCTCCTGCCAGGTTGTTGGGTGGACATTGAGCCCTGTAGGCGCGGGTTTACCCGCGAATGCGGAGGTATAGCCACCATCGCATTCGCGGGTAAA‑CCGCTCCTACACAGAGCCCGCCACCCAAGCCAGGTGGCGGGGAGGGCTATCAGGCGTCCTGATAGCTCTCGATCGACGGGCAGGCGCACACCAGGTTGCGGTCGCCGAACACGTTGTCGACCCGGCCGACCGGCGGCCAGTACTTGCC > NC_002947_CJ‑RC/1126529‑1126793
|
| 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: ‑ |
