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 |
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 | 92.3%
| 37.0
/ ‑2.6
| 13 | intergenic (‑99/+50) | tdcG‑II/gcvP‑I | L‑serine dehydratase/glycine dehydrogenase |
| Reads supporting (aligned to +/- strand): ref base . (1/0); new base C (7/5); total (8/5) |
| Fisher's exact test for biased strand distribution p-value = 1.00e+00 |
| Kolmogorov-Smirnov test that lower quality scores support variant p-value = 8.15e-01 |
GAGGGGCCGATGCCGATCTTGAACAGGTCGAAGACGCTCAGTGACATGTGGACCTCCTGCCAGGTTGTTGGGTGGACATTGAGCCCTGTAGGCGCGGGTTTACCCGCGAATGCGGAGGTATAGCCACCATCGCATTCGCGGG‑TAAA‑‑CCGCTCCTACACAGAGCCCGCCACCCAAGCCAGGTGGCGGGGAGGGCTATCAGGCGTCCTGATAGCTCTCGATCGACGGGCAGGCGCACACCAGGTTGCGGTCGCCGAACACGTTGTCGACCCGGCCGACCGGCGGC > NC_002947_CJ‑RC/1126500‑1126782
|
gAGGGGCCGATGCCGATCTTGAACAGGTCGAAGACGCTCAGTGACATGTGGACCTCCTGCCAGGTTGTTGGGTGGACATTGAGCCCTGTAGGCGCGGGTTTACCCGCGAATGCGGAGGTATAGCCACCATCGCATTCGCGGG‑TAAA‑‑cc < 5:327260/148‑1 (MQ=255)
cgGGTTTACCCGCGAATGCGGAGGTATAGCCACCATCGCATTCGCGGG‑TAAAC‑CCGCTCCTACACAGAGCCCGCCACCCAAGCCAGGTGGCGGGGAGGGCTATCAGGCGTCCTGATAGCTCTCGATCGACGGGCAGGCGCACACCAgg > 5:151152/1‑148 (MQ=255)
cgGGTTAACCCGCTAATGCGGAGGTATACCCACCATCGCATGCGGGGT‑AAAAC‑CCGCTCCTACACAGAGCCCGCCACCCAAGCCAGGTGGCGGGGAGGGCTATCAGGCGTCCTGATAGCTCTCGATCGACGGGCAGGCGCACACCAGGt < 8:216100/149‑1 (MQ=255)
ttACCCGCGAATGCGGAGGTATAGCCACCATCGCATTCGCGGGTTAAC‑‑CCGCTCCTACACAGAGCCCGCCACCCAAGCCAGGTGGCGGGGAGGGCTATCAGGCGTCCTGATAGCTCTCGATCGACGGGCAGGCGCACACCAGGTTGCg > 3:21348/1‑148 (MQ=255)
cgcgAATGCGGAGGTATAGCCACCATCGCATTCGCGGG‑TAAAC‑CCGCTCCTACACAGAGCCCGCCACCCAAGCCAGGTGGCGGGGAGGGCTATCAGGCGTCCTGATAGCTCTCGATCGACGGGCAGGCGCACACCAGGTTGCGGTCGc > 6:49887/1‑148 (MQ=255)
cgAATGCGGAGGTATAGCCACCATCGCATTCGCGGG‑TAAAC‑CCGCTCCTACACAGAGCCCGCCACCCAAGCCAGGTGGCGGGGAGGGCTATCAGGCGTCCTGATAGCTCTCGATCGACGGGCAGGCGCACACCAGGTTGCGGTCGcc > 1:252409/1‑147 (MQ=255)
gAGGTATAGCCACCATCGCATTCGCGGG‑TAAAC‑CCGCTCCTACACAGAGCCCGCCACCCAAGCCAGGTGGCGGGGAGGGCTATCAGGCGTCCTGATAGCTGTCGATCGACGGGCAGGCGCCCACCAGGTTGCGGTCGCCGAACACGtt > 1:350330/1‑148 (MQ=255)
gAGGTATAGCCACCATCGCATTCGCGGG‑TAAAC‑CCGCTCCTACACAGAGCCCGCCACCCAAGCCAGGTGGCGGGGAGGGCTATCAGGCGTCCTGATAGCTCTCGATCGACGGGCAGGCGCACACCAGGTTGCGGTCGCCGAACACGtt < 5:49887/148‑1 (MQ=255)
caccaTCGCATTCGCGGG‑TAAAC‑CCGCTCCTACACAGAGCCCGCCACCCAAGCCAGGTGGCGGGGAGGGCTATCAGGCGTCCTGATAGCTCTCGATCGACGGGCAGGCGCACACCAGGTTGCGGTCGCCGAACACGTTGTCGACCCgg > 3:271165/1‑148 (MQ=255)
cATTCGCGGT‑TAAAC‑CCGCTCCTACACAGAGCCCGCCACCCAAGCCAGGTGGCGGGGAGGGCTATCAGGCGTCCTGATAGCTCTCGATCGACGGGCAGGCGCACACCAGGTTGCGGTCGCCGAACACGTTGTCGACCCGGCCGACcggc < 7:118534/149‑1 (MQ=255)
atcccgGG‑TAAACCCCGCTCCTACACAGAGCCCGCCACCCAAGCCAGGTGGCGGGGAGGGCTATCAGGCGTCCTGATAGCTCTCGATCGACGGGCAGGCGCACACCAGGTTGCGGTCGCCGAACACGTTGTCGACCCGGCCGACcggc < 5:71423/144‑1 (MQ=255)
cgcgGG‑TAAAC‑CCGCTCCTACACAGAGCCCGCCACCCAAGCCAGGTGGCGGGGAGGGCTATCAGGCGTCCTGATAGCTCTCGATCGACGGGCAGGCGCACACCAGGTTGCGGTCGCCGAACACGTTGTCGACCCGGCCGACCggcggc > 6:35360/1‑148 (MQ=255)
gcgGG‑TAAAC‑CCGCTCCTACACAGAGCCCGCCACCCAAGCCAGGTGGCGGGGAGGGCTATCAGGCGTCCTGATAGCTCTCGATCGACGGGCAGGCGCACACCAGGTTGCGGTCGCCGAACACGTTGTCGAccc < 7:260570/133‑1 (MQ=255)
gcgGG‑TAAAC‑CCGCTCCTACACAGAGCCCGCCACCCAAGCCAGGTGGCGGGGAGGGCTATCAGGCGTCCTGATAGCTCTCGATCGACGGGCAGGCGCACACCAGGTTGCGGTCGCCGAACACGTTGTCGAccc > 8:260570/1‑133 (MQ=255)
|
GAGGGGCCGATGCCGATCTTGAACAGGTCGAAGACGCTCAGTGACATGTGGACCTCCTGCCAGGTTGTTGGGTGGACATTGAGCCCTGTAGGCGCGGGTTTACCCGCGAATGCGGAGGTATAGCCACCATCGCATTCGCGGG‑TAAA‑‑CCGCTCCTACACAGAGCCCGCCACCCAAGCCAGGTGGCGGGGAGGGCTATCAGGCGTCCTGATAGCTCTCGATCGACGGGCAGGCGCACACCAGGTTGCGGTCGCCGAACACGTTGTCGACCCGGCCGACCGGCGGC > NC_002947_CJ‑RC/1126500‑1126782
|
| 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
GGAGGGGCCGATGCCGATCTTGAACAGGTCGAAGACGCTCAGTGACATGTGGACCTCCTGCCAGGTTGTTGGGTGGACATTGAGCCCTGTAGGCGCGGGTTTACCCGCGAATGCGGAGGTATAGCCACCATCGCATTCGCGGG‑TAAA‑‑CCGCTCCTACACAGAGCCCGCCACCCAAGCCAGGTGGCGGGGAGGGCTATCAGGCGTCCTGATAGCTCTCGATCGACGGGCAGGCGCACACCAGGTTGCGGTCGCCGAACACGTTGTCGACCCGGCCGACCGGCGGCCAGTACTTGCC > NC_002947_CJ‑RC/1126499‑1126793
|
GGAGGGGCCGATGCCGATCTTGAACAGGTCGAAGACGCTCAGTGACATGTGGACCTCCTGCCAGGTTGTTGGGTGGACATTGAGCCCTGTAGGCGCGGGTTTACCCGCGAATGCGGAGGTATAGCCACCATCGCATTCGCGGG‑TAAA‑‑CCcg < NB501016:282:H2V7GAFX2:3:21605:24121:8119/151‑3 (MQ=60)
cccgctctgtcaattgtgccccccctccctgttttttggggtcaattgccgcccttacggcgggttttacccggctatgggggagtaaaccccaccagccattgcgggttaaaccCCGCTCCTACACAGAGCCCGCCACCCAAGCCAGGTG < NB501016:282:H2V7GAFX2:4:11405:12960:17867/36‑1 (MQ=60)
cgccgggcgccccggccgtgggggtcgccctgctccaccccccgctgcttcgccgtccgcttgcgctccgcgttccactcccccattgtctggccgaaacaccccCCGCTCCTACACAGAGCCCGCCACCCAAGCCAGGGGGCGGGGAGG < NB501016:282:H2V7GAFX2:1:11310:25105:10792/45‑1 (MQ=60)
gcgcccccccccgcggctggtgggggctacttgcgcccgtctggggggggcacccccgggcatcgcgctgttaccccccccccccacggggggttaaaccCCGCTCCTACACAGAGCCCGCCACCCAAGCCAGGTGGCGGGGAGGGCTATC < NB501016:282:H2V7GAFX2:4:21611:12349:9037/51‑1 (MQ=60)
ccgggcgtttttgggggcatcaaatcccgcctgtgggggggggtcacccgcggtttggtggcttaccccccacaagctaaggggttaaaaaccCCGCTCCTACACAGAGCCCGCCACCCAAGCCAGGTGGCGGGGAGGGCTATCAGGCG < NB501016:282:H2V7GAFX2:1:21102:1531:8939/56‑1 (MQ=60)
gggcgaaattgtccccttcccggcgggtataccccggatacggggtgtttaaaccaccactcCATTCGGGGG‑TAAACCCCGCTCCTACACAGAGCCCGCCACCCAAGCCAGGTGGCGGGGAGGGCTATCAGGCGTCCTGATAGCTCTCGAT < NB501016:282:H2V7GAFX2:4:21509:8608:2313/89‑1 (MQ=60)
CGCGGGTTTACCCGCGAATGCGGAGGTATAGCCACCATCGCATTCGCGGG‑TAAAC‑CCGCTCCTACACAGAGCCCGCCACCCAAGCCAGGTGGCGGGGAGGGCTATCAGGCGTCCTGATAGCTCTCGATCGACGGGCAGGCGCACACCAGGT > NB501016:282:H2V7GAFX2:3:11606:3464:6917/1‑151 (MQ=60)
GTTTACCCGCGAATGCGGAGGTATAGCCACCATCGCATTCGCGGGTTAAC‑‑CCGCTCCTACACAGAGCCCGCCACCCAAGCCAGGTGGCGGGGAGGGCTATCAGGCGTCGTGATAGCTCTCGATCGACGGGCAGGCGCACACCAGGTTGCGG > NB501016:282:H2V7GAFX2:2:11105:21862:7588/1‑151 (MQ=60)
CCGCGAATGCGGAGGTATAGCCACCATCGCATTCGCGGG‑TAAA‑‑CC > NB501016:282:H2V7GAFX2:4:21607:26665:5016/1‑45 (MQ=60)
CGCGAATGCGGAGGTATAGCCACCATCGCATTCGCGGG‑TAAAC‑CCGCTCCTACACAGAGCCCGCCACCCAAGCCAGGTGGCGGGGAGGGCTATCAGGCGTCCTGATAGCTCTCGATCGACGGGCAGGCGCACACCAGGTTGCGGTCGCCG > NB501016:282:H2V7GAFX2:1:21201:14763:13906/1‑150 (MQ=60)
CGGAGGTATAGCCACCATCGCATTCGCGGG‑TAAAC‑CCGCTCCTACACAGAGCCCGCCACCCAAGCCAGGTGGCGGGGAGGGCTATCAGGCGTCCTGATAGCTGTCGATCGACGGGCAGGCGCCCACCAGGTTGCGGTCGCCGAACACGTTT > NB501016:282:H2V7GAFX2:1:21310:21632:2810/1‑151 (MQ=60)
GGAGGTATAGCCACCATCGCATTCGCGGG‑TAAAC‑CCGCTCCTACACAGAGCCCGCCACCCAAGCCAGGTGGCGGGGAGGGCTATCAGGCGTCCTGATAGCTCTCGATCGACGGGCAGGCGCACACCAGGTTGCGGTCGCCGAACACGTTGT < NB501016:282:H2V7GAFX2:3:11411:19363:4084/151‑1 (MQ=60)
GCCACCATCGCATTCGCGGG‑TAAAC‑CCGCTCCTACACAGAGCCCGCCACCCAAGCCAGGTGGCGGGGAGGGCTATCAGGCGTCCTGATAGCTCTCGATCGACGGGCAGGCGCACACCAGGTTGCGGTCGCCGAACACGTTGTCGACCCGGC > NB501016:282:H2V7GAFX2:2:21208:4789:16364/1‑151 (MQ=60)
CCATTCGCGGT‑TAAAC‑CCGCTCCTACACAGAGCCCGCCACCCAAGCCAGGTGGCGGGGAGGGCTATCAGGCGTCCTGATAGCTCTCGATCGACGGGCAGGCGCACACCAGGTTGCGGTCGCCGAACACGTTGTCGACCCGGCCGACCGGCG < NB501016:282:H2V7GAFX2:4:11511:20443:9630/151‑1 (MQ=60)
catcccgggtaaaccCCGCTCCTACACAGAGCCCGCCACCCAAGCCAGGTGGCGGGGAGGGCTATCAGGCGTCCTGATAGCTCTCGATCGACGGGCAGGCGCACACCAGGTTGCGGTCGCCGAACACGTTGTCGACCCGGCCGACCGGCGG < NB501016:282:H2V7GAFX2:3:11503:26469:7867/136‑1 (MQ=60)
CGCGGG‑TAAAC‑CCGCTCCTACACAGAGCCCGCCACCCAAGCCAGGTGGCGGGGAGGGCTATCAGGCGTCCTGATAGCTCTCGATCGACGGGCAGGCGCACACCAGGTTGCGGTCGCCGAACACGTTGTCGACCCG < NB501016:282:H2V7GAFX2:4:21503:4053:2542/135‑1 (MQ=60)
GG‑TAAAC‑CCGCTCCTACACAGAGCCCGCCACCCAAGCCAGGTGGCGGGGAGGGCTATCAGGCGTCCTGATAGCTCTCGATCGACGGGCAGGCGCACACCAGGTTGCGGTCGCCGAACACGTTGTCGACCCGGCCGACCGGCGGCCAGTACT > NB501016:282:H2V7GAFX2:2:21108:16312:16291/1‑151 (MQ=60)
GG‑TAAAC‑CCGCTCCTACACAGAGCCCGCCACCCAAGCCAGGTGGCGGGGAGGGCTATCAGGCGTCCTGATAGCTCTCGATCGACGGGCAGGCGCACACCAGGTTGCGGTCGCCGAACACGTTGTC < NB501016:282:H2V7GAFX2:3:21411:11208:16886/125‑1 (MQ=60)
AAC‑‑CCGCTCCTACACAGAGCCCGCCACCCAAGCCAGGTGGCGGGGAGGGCTATCAGGCGTCCTGATAGCTCTCGATCGACGGGCAGGCGCACACCAGGTTGCGGTCGCCGAACACGTTGTCGACCCGGCCGACCGGCGGCCAGTACTTGCC < NB501016:282:H2V7GAFX2:1:21209:8770:4079/151‑1 (MQ=60)
AAC‑‑CCGCTCCTACACAGAGCCCGCCACCCAAGCCAGGTGGCGGGGAGGGCTATCAGGCGTCCTGAT < NB501016:282:H2V7GAFX2:3:21603:1527:11235/66‑1 (MQ=60)
|
GGAGGGGCCGATGCCGATCTTGAACAGGTCGAAGACGCTCAGTGACATGTGGACCTCCTGCCAGGTTGTTGGGTGGACATTGAGCCCTGTAGGCGCGGGTTTACCCGCGAATGCGGAGGTATAGCCACCATCGCATTCGCGGG‑TAAA‑‑CCGCTCCTACACAGAGCCCGCCACCCAAGCCAGGTGGCGGGGAGGGCTATCAGGCGTCCTGATAGCTCTCGATCGACGGGCAGGCGCACACCAGGTTGCGGTCGCCGAACACGTTGTCGACCCGGCCGACCGGCGGCCAGTACTTGCC > NC_002947_CJ‑RC/1126499‑1126793
|
| 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: ‑ |
