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 F14 I1 R1
|
58 |
76.7 |
3323998 |
98.6% |
3277462 |
146.9 |
Breseq alignment
BRESEQ :: Evidence
|
| evidence |
seq id |
position |
mutation |
annotation |
gene |
description |
| RA |
NC_002947_CJ‑RC |
1,419,549 |
+C |
intergenic (‑38/+98) |
PP_1242 ← / ← PP_1244 |
hypothetical protein/hypothetical protein |
|
| |
seq id |
position |
ref |
new |
freq |
score (cons/poly) |
reads |
annotation |
genes |
product |
| * | NC_002947_CJ‑RC | 1,419,548 | 1 | . | C | 94.4%
| 58.2
/ ‑3.0
| 18 | intergenic (‑37/+99) | PP_1242/PP_1244 | hypothetical protein/hypothetical protein |
| Reads supporting (aligned to +/- strand): ref base . (0/1); new base C (3/14); total (3/15) |
| Fisher's exact test for biased strand distribution p-value = 1.00e+00 |
| Kolmogorov-Smirnov test that lower quality scores support variant p-value = 9.93e-01 |
CTGGCAGGGGATGCCGGGTTCGATGCGGAACAGCGGGTGAGTGTTGTTTTCGCCTTGGTAGAAGCAGGTCTTGCCGACTGTGGTGGG‑TTCTGTTGTGTTGTCGGTGGGCATTGTTTTGTTTCCCTGGATTCTGGGTTGCCTGGGCTG‑G‑CTCTTCGCGGGCACGCCCGCTCCCACAGGTACTGTGCAGTGCGTGACGGCTGTGGTGACCCTGTGGGAGC > NC_002947_CJ‑RC/1419401‑1419618
|
cTGGCAGGGGATGCCGGGTTCGATGCGGAACAGCGGGTGAGTGTTGTTTTCGCCTTGGTAGAAGCAGGTCTTGCCGACTGTGGTGGG‑TTCTGTTGTGTTGTCGGTGGGCATTGTTTTGTTTCCCTGGATTCTGGGTTGCCTGggctg‑g < 2:9178/148‑1 (MQ=255)
aGGGGATGCCGGGTTCGATGCGGAACAGCGGGTGAGTGTTGTTTTCGCCTTGGTAGAAGCAGGTCTTGCCGACTGTGGTGGG‑TTCTGTTGTGTTGTCGGTGGGCATTGTTTTGTTTCCCTGGATTCTGGGTTGCCTGggctg‑g‑cctctt < 5:7732/149‑6 (MQ=255)
cGGGTGAGTGTTGTTTTCGCCTTGGTAGAAGCAGGTCTTGCCGACTGTGGTGGG‑TTCTGTTGTGTTGTCGGTGGGCATTGTTTTGTTTCCCTGGATTCTGGGTTGCCTGGGCTG‑GCCTCTTCGCGGGCACGCCCGCTCCCACAGGTACt < 5:212289/149‑1 (MQ=255)
gTGAGTGTTGTTTTCGCCTTGGTAGAAGCAGGTCTTGCCGACTGTGGTGGG‑TTCTGTTGTGTTGTCGGTGGGCATTGTTTTGTTTCCCTGGATTCTGGGTTGCCTGGGCTG‑GCCTCTTCGCGGGCACGCCCGCTCCCACAGGTACtgtg < 2:6361/149‑1 (MQ=255)
aGTGTTGTTTTCGCCTTGGTAGAAGCAGGTCTTGCCGACTGTGGTGGG‑TTCTGTTGTGTTGTCGGTGGGCATTGTTTTGTTTCCCTGGATTCTGGGTTGCCTGGGCTG‑GCCTCTTCGCGGGCACGCCCGCTCCCACAGGTACTGTGCa < 5:95827/148‑1 (MQ=255)
gtgtTGTTTTCGCCTTGGTAGAAGCAGGTCTTGCCGACTGTGGTGGG‑TTCTGTTGTGTTGTCGGTGGGCATTGTTTTGTTTCCCTGGATTCTGGGTTGCCTGGGCTG‑GCCTCTTCGCGGGCACGCCCGCTCCCACAGGTACTGTGCAGt < 7:44618/149‑1 (MQ=255)
ttgttTTCGCCTTGGTAGAAGCAGGTCTTGCCGACTGTGGTGGG‑TTCTGTTGTGTTGTCGGTGGGCATTGTTTTGTTTCCCTGGATTCTGGGTTGCCTGGGCTG‑GCCTCTTCGCGGGCACGCCCGCTCCCACAGGTACTGTGCAGTGc < 1:410532/148‑1 (MQ=255)
gttTTCGCCGTGGTAGAATCCGGGATTGCCGACTG‑GGTGGGTTTCTGTTGTGTTGTCGGTTGGCATTGTTTTGTTTCCCTGGAGTCTGGGTTGCCTGGGCTGTC‑CTCTTCGCTGGCACGCCCGCTCCCACAGGTACTGTGCAGTGCGt < 2:160232/148‑1 (MQ=255)
ttCGCCTTGGTAGAAGCAGGTCTTGCCGACTGTGGTGGG‑TTCTGTTGTGTTGTCGGTGGGCATTGTTTTGTTTCCCTGGATTCTGGGTTGCCTGGGCTG‑GCCTCTTCGCGGGCACGCCCGCTCCCACAGGTACTGTGCAGTGCGTGACg > 7:15709/1‑149 (MQ=255)
tCGCCTTGGTAGAAGCAGGTCTTGCCGACTGTGGTGGG‑TTCTGTTGTGTTGTCGGTGGGCATTGTTTTGTTTCCCTGGATTCTGGGTTGCCTGGGCTG‑GCCTCTTCGCGGGCACGCCCGCTCCCACAGGTACTGTGCAGTGCGTGACg < 2:229519/148‑1 (MQ=255)
cTTGGTAGAAGCAGGTCTTGCCGACTGTGGTGGG‑TTCTGTTGTGTTGTCGGTGGGCATTGTTTTGTTTCCCTGGATTCTGGGTTGCCTGGGCTG‑GCCTCTTCGCGGGCAc < 3:93810/110‑1 (MQ=255)
cTTGGTAGAAGCAGGTCTTGCCGACTGTGGTGGG‑TTCTGTTGTGTTGTCGGTGGGCATTGTTTTGTTTCCCTGGATTCTGGGTTGCCTGGGCTG‑GCCTCTTCGCGGGCAc > 4:93810/1‑110 (MQ=255)
ttGGTAGAAGCAGGTCTTGCCGACTGTGGTGGG‑TTCTGTTGTGTTGTCGGTGGGCATTGTTTTGTTTCCCTGGATTCTGGGTTGCCTGGGCTG‑GCCTCTTCGCGGGCACGCCCGCTCCCACAGGTACTGTGCAGTGCGTGACGGCtgtg < 3:215457/149‑1 (MQ=255)
tAGAAGCAGGTCTTGCCGACTGTGGTGGG‑TTCTGTTGTGTTGTCGGTGGGCATTGTTTTGTTTCCCTGGATTCTGGGTTGCCTGGGCTG‑GCCTCTTCGCGGGCACGCCCGCTCCCACAGGTACTGTGCAGTGCGTGACGGCTGTGGTGa < 8:233763/149‑1 (MQ=255)
aGGTCTTGCCGACTGTGGTGGG‑TTCTGTTGTGTTGTCGGTGGGCATTGTTTTGTTTCCCTGGATTCTGGGTTGCCTGGGCTG‑GCCTCTTCGCGGGCACGCCCGCTCCCACAGGTACTGTGCAGTGCGTGACGGCTGTGGTGACGCtgtg < 2:43764/149‑1 (MQ=255)
ggTCTTGCCGACTGTGGTGGG‑TTCTGTTGTGTTGTCGGTGGGCATTGTTTTGTTTCCCTGGATTCTGGGTTGCCTGGGCTG‑GCCTCTTCGCGGGCACGCCCGCTCCCACAGGTACTGTGCAGTGCGTGACGGCTGTGGTGACCCTGTgg < 2:401694/149‑1 (MQ=255)
tCTTGCCGACTGTGGTGGG‑TTCTGTTGTGTTGTCGGTGGGCATTGTTTTGTTTCCCTGGATTCTGGGTTGCCTGGGCTG‑GCCTCTTCGCGGGCACGCCCGCTCCCACAGGTACTGTGCAGTGCGTGACGGCTGTGGTGACCCTGTGGGa < 1:213806/149‑1 (MQ=255)
gCCGACTGTGGTGGG‑TTCTGTTGTGTTGTCGGTGGGCATTGTTTTGTTTCCCTGGATTCTGGGTTGCCTGGGCTG‑GCCTCTTCGCGGGCACGCCCGCTCCCACAGGTACTGTGCAGTGCGTGACGGCTGTGGTGACCCTGTGGGAGc < 8:15709/147‑1 (MQ=255)
gACTGTGGTGGG‑TTCTGTTGTGTTGTCGGTGGGCATTGTTTTGTTTCCCTGGATTCTGGGTTGCCTGGGCTG‑GCCTCTTCGCGGGCACGCCCGCTCCCACAGGTACTGTGCAGTGCGTGACGGCTGTGGTGACCCtgt < 4:146573/138‑1 (MQ=255)
gACTGTGGTGGG‑TTCTGTTGTGTTGTCGGTGGGCATTGTTTTGTTTCCCTGGATTCTGGGTTGCCTGGGCTG‑GCCTCTTCGCGGGCACGCCCGCTCCCACAGGTACTGTGCAGTGCGTGACGGCTGTGGTGACCCtgt > 3:146573/1‑138 (MQ=255)
|
CTGGCAGGGGATGCCGGGTTCGATGCGGAACAGCGGGTGAGTGTTGTTTTCGCCTTGGTAGAAGCAGGTCTTGCCGACTGTGGTGGG‑TTCTGTTGTGTTGTCGGTGGGCATTGTTTTGTTTCCCTGGATTCTGGGTTGCCTGGGCTG‑G‑CTCTTCGCGGGCACGCCCGCTCCCACAGGTACTGTGCAGTGCGTGACGGCTGTGGTGACCCTGTGGGAGC > NC_002947_CJ‑RC/1419401‑1419618
|
| Alignment Legend |
|---|
Aligned base mismatch/match (shaded by quality score): ATCG/ATCG < 3 ≤ ATCG/ATCG < 14 ≤ 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
CAGGGGATGCCGGGTTCGATGCGGAACAGCGGGTGAGTGTTGTTTTCGCCTTGGTAGAAGCAGGTCTTGCCGACTGTGGTGGGTTCTGTTGTGTTGTCGGTGGGCATTGTTTTGTTTCCCTGGATTCTGGGTTGCCTGGGCTGG‑CTCTTCGCGGGCACGCCCGCTCCCACAGGTACTGTGCAGTGCGTGACGGCTGTGGTGACCCTGTGGGAGCGGGCGTGCCCGCGAAGAGGCCTGACCTGCTAATGCAAGG > NC_002947_CJ‑RC/1419405‑1419657
|
CAGGGGATGCCGGGTTCGATGCGGAACAGCGGGTGAGTGTTGTTTTCGCCTTGGTAGAAGCAGGTCTTGCCGACTGTGGTGGGTTCTGTTGTGTTGTCGGTGGGCATTGTTTTGTTTCCCTGGATTCTGGGTTGCCTGGGCTGGCCTCTTC < NB501016:282:H2V7GAFX2:3:11402:23203:7984/151‑1 (MQ=60)
CGATGCGGAACAGCGGGTGAGTGTTGTTTTCGCCTTGGTAGAAGCAGGTCTTGCCGACTGTGGTGGGTTCTGTTGTGTTGTCGGTGGGCATTGTTTTGTTTCCCTGGATTCTGGGTTGCCTGGGCTGG‑Ccaattagccggggccccccccc > NB501016:282:H2V7GAFX2:4:21405:9288:9881/1‑129 (MQ=60)
GATGCGGAACAGCGGGTGAGTGTTGTTTTCGCCTTGGTAGAAGCAGGTCTTGCCGACTGTGGTGGGTTCTGTTGTGTTGTCGGTGGGCATTGTTTTGTTTCCCTGGATTCTGGGTTGCCTGGGCTGG‑Cccaatagcgcggggccccccccc > NB501016:282:H2V7GAFX2:2:21209:26820:14604/1‑128 (MQ=60)
GATGCGGAACAGCGGGTGAGTGTTGTTTTCGCCTTGGTAGAAGCAGGTCTTGCCGACTGTGGTGGGTTCTGTTGTGTTGTCGGTGGGCATTGTTTTGTTTCCCTGGATTCTGGGTTGCCTGGGCTGG‑Ccacataagcggggggcccccccc > NB501016:282:H2V7GAFX2:2:21208:1320:14609/1‑128 (MQ=60)
GCGGGTGAGTGTTGTTTTCGCCTTGGTAGAAGCAGGTCTTGCCGACTGTGGTGGGTTCTGTTGTGTTGTCGGTGGGCATTGTTTTGTTTCCCTGGATTCTGGGTTGCCTGGGCTGGCCTCTTCGCGGGCACGCCCGCTCCCACAGGTACTG < NB501016:282:H2V7GAFX2:3:11612:3813:11443/151‑1 (MQ=60)
GAGTGTTGTTTTCGCCTTGGTAGAAGCAGGTCTTGCCGACTGTGGTGGGTTCTGTTGTGTTGTCGGTGGGCATTGTTTTGTTTCCCTGGATTCTGGGTTGCCTGGGCTGGCCTCTTCGCGGGCACGCCCGCTCCCACAGGTACTGTGCAG < NB501016:282:H2V7GAFX2:3:11505:24406:16662/150‑1 (MQ=60)
AGTGTTGTTTTCGCCTTGGTAGAAGCAGGTCTTGCCGACTGTGGTGGGTTCTGTTGTGTTGTCGGTGGGCATTGTTTTGTTTCCCTGGATTCTGGGTTGCCTGGGCTGGCCTCTTCGCGGGCACGCCCGCTCCCACAGGTACTGTGCAGTG < NB501016:282:H2V7GAFX2:4:11408:8759:7059/151‑1 (MQ=60)
GTGTTGTTTTCGCCTTGGTAGAAGCAGGTCTTGCCGACTGTGGTGGGTTCTGTTGTGTTGTCGGTGGGCATTGTTTTGTTTCCCTGGATTCTGGGTTGCCTGGGCTGG‑Ccgcatagccgggggcccccccccccccccgggaggggggggg > NB501016:282:H2V7GAFX2:4:21501:4933:10210/1‑109 (MQ=60)
GTTGTTTTCGCCTTGGTAGAAGCAGGTCTTGCCGACTGTGGTGGGTTCTGTTGTGTTGTCGGTGGGCATTGTTTTGTTTCCCTGGATTCTGGGTTGCCTGGGCTGGCCTCTTCGCGGGCACGCCCGCTCCCACAGGTACTGTGCAGTGCG < NB501016:282:H2V7GAFX2:1:21311:8473:16941/150‑1 (MQ=60)
GTTTTCGCCTTGGTAGAAGCAGGTCTTGCCGACTGTGGTGGGTTCTGTTGTGTTGTCGGTGGGCATTGTTTTGTTTCCCTGGATTCTGGGTTGCCTGGGCTGG‑Ccaaaaaaccggcgggcccccccccccccaccgcgtgtggggcggggc > NB501016:282:H2V7GAFX2:4:11610:20337:18401/1‑104 (MQ=60)
TTTTCGCCTTGGTAGAAGCAGGTCTTGCCGACTGTGGTGGGTTCTGTTGTGTTGTCGGTGGGCATTGTTTTGTTTCCCTGGATTCTGGGTTGCCTGGGCTGG‑Cctattagcggggcccccccccccccccacggaggttgttggggggggg > NB501016:282:H2V7GAFX2:3:21602:17068:9865/1‑103 (MQ=60)
TTTCGCCTTGGTAGAAGCAGGTCTTGCCGACTGTGGTGGGTTCTGTTGTGTTGTCGGTGGGCATTGTTTTGTTTCCCTGGATTCTGGGTTGCCTGGGCTGGCCTCTTCGCGGGCACGCCCGCTCCCACAGGTACTGTGCAGTGCGTGACGG > NB501016:282:H2V7GAFX2:4:11403:8537:13247/1‑151 (MQ=60)
TTCGCCTTGGTAGAAGCAGGTCTTGCCGACTGTGGTGGGGTCTGTTGTGTTGTCGGTGGGCATTGTTTTGTTTCCCTGGATTCTGGGTTGCCTGGGCTGGCCTCTTCGCGGGCACGCactgcacagtacctgtgggagcgggcgtgcccg < NB501016:282:H2V7GAFX2:4:11409:4891:20056/150‑34 (MQ=60)
CCTTGGTAGAAGCAGGTCTTGCCGACTGTGGTGGGTTCTGTTGTGTTGTCGGTGGGCATTGTTTTGTTTCCCTGGATTCTGGGTTGCCTGGGCTGGCCTCTTCGCGGGCACG < NB501016:282:H2V7GAFX2:2:11205:14352:9918/112‑1 (MQ=60)
GTTGGTAGAAGCAGGTCTTGCCGACTGTGGTGGGTTCTGTTGTGTTGTCGGTGGGCATTGTTTTGTTTCCCTGGATTCTGGGTTGCCTGGGCTGGCCTCTTCGCGGGCACGCCCGCTCCCACAGGTACTGTGCAGTGCGTGACGGCTGTGG < NB501016:282:H2V7GAFX2:2:21101:14990:15194/151‑1 (MQ=60)
GTCTTGCCGACTGTGGTGGGTTCTGTTGTGTTGTCGGTGGGCATTGTTTTGTTTCCCTGGATTCTGGGTTGCCTGGGCTGGCCTCTTCGCGGGCACGCCCGCTCCCACAGGgtcaccacagccgtcacgcactgcacagtacctgtgggag < NB501016:282:H2V7GAFX2:2:21303:6441:18517/151‑41 (MQ=60)
GTCTTGCCGACTGTGGTGGGTTCTGTTGTGTTGTCGGTGGGCATTGTTTTGTTTCCCTGGATTCTGGGTTGCCTGGGCTGGCCTCTTCGCGGGCACGCCCGCTCCCACAGGTACTGTGCAGTGCGTGACGGCTGTGGTGACCCTGTGGGAG < NB501016:282:H2V7GAFX2:1:11312:11982:12380/151‑1 (MQ=60)
CGACTGTGGTGGGTTCTGTTGTGTTGTCGGTGGGCATTGTTTTGTTTCCCTGGATTCTGGGTTGCCTGGGCTGGCCTCTTCGCGGGCACGCCCGCTCCCACAGGTACTGTGCAGTGCGTGACGGCTGTGGTGACCCTGTG > NB501016:282:H2V7GAFX2:2:11302:7360:9422/1‑140 (MQ=60)
TGTTGTCGGTGGGCATTGTTTTGTTTCCCTGGATTCTGGGTTGCCTGGGCTGG‑Cccgaaaaagcggcgcggccccccccacccccaccaggatgtaggggaggcgggggtgggtgtcgtcggagggggcgcgggccgcgcacacgccacc > NB501016:282:H2V7GAFX2:1:21102:22907:6467/1‑54 (MQ=60)
GCATTGTTTTGTTTCCCTGGATTCTGGGTTGCCTGGGCTGG‑Ccgcatttcgggggggcccccccccaaacccttaaattggtaggggggggggggggtgggggccggggggggggggggggggggcgcccgggcggcgcgcggaataaaa > NB501016:282:H2V7GAFX2:4:11607:3176:7749/1‑42 (MQ=60)
CTCTTCGCGGGCACGCCCGCTCCCACAGGTACTGTGCAGTGCGTGACGGCTGTGGTGACCCTGTGGGAGCGGG < NB501016:282:H2V7GAFX2:1:11206:15525:5740/73‑1 (MQ=60)
|
CAGGGGATGCCGGGTTCGATGCGGAACAGCGGGTGAGTGTTGTTTTCGCCTTGGTAGAAGCAGGTCTTGCCGACTGTGGTGGGTTCTGTTGTGTTGTCGGTGGGCATTGTTTTGTTTCCCTGGATTCTGGGTTGCCTGGGCTGG‑CTCTTCGCGGGCACGCCCGCTCCCACAGGTACTGTGCAGTGCGTGACGGCTGTGGTGACCCTGTGGGAGCGGGCGTGCCCGCGAAGAGGCCTGACCTGCTAATGCAAGG > NC_002947_CJ‑RC/1419405‑1419657
|
| 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: ‑ |
