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 |
|
A5 F18 I1 R1
|
59 |
77.7 |
3515218 |
98.5% |
3462489 |
145.9 |
Breseq alignment
BRESEQ :: Evidence
|
| evidence |
seq id |
position |
mutation |
annotation |
gene |
description |
| RA |
NC_002947_CJ‑RC |
278,744 |
+A |
intergenic (‑239/+75) |
PP_0224 ← / ← sctC |
DszC family monooxygenase/sulfur compound ABC transporter ATP‑binding protein |
|
| |
seq id |
position |
ref |
new |
freq |
score (cons/poly) |
reads |
annotation |
genes |
product |
| * | NC_002947_CJ‑RC | 278,742 | 1 | . | A | 77.3%
| 54.2
/ 12.5
| 22 | intergenic (‑237/+77) | PP_0224/sctC | DszC family monooxygenase/sulfur compound ABC transporter ATP‑binding protein |
| Reads supporting (aligned to +/- strand): ref base . (3/2); new base A (3/14); total (6/16) |
| Fisher's exact test for biased strand distribution p-value = 1.00e-01 |
| Kolmogorov-Smirnov test that lower quality scores support variant p-value = 1.00e+00 |
ATGTCGCTACAGCTGATCGCGACAGACGTGTGCTGGTCCGGTGGTCCGG‑‑TATATATACCCTAATGATTTATAAAATTTTTATGAACTAACTTTTTGGAATATTTATAGAAGGGGGATTTGTTACAGAGGTGCCGGGCTCTTCGC‑GGG‑T‑AA‑CCCGCTCCTACACACATGCCTCAAGATCTGTGCACTGTAGGAGCGGGTTTACCCGCGAAAGGGCCGGAACAGGTTTACTCGGAGGCCGCAGTCCCGAGGAACTTGCGCAAGAACTGCCGCGTACGCTCTTC > NC_002947_CJ‑RC/278595‑278875
|
ttGTCTCTACAGCTTATCGCGACAGTCGTTTGCTGGTCCGGTGGTCCGG‑‑TAAATTTACCCTAAATATTTATAAAATTTTTATTAACTAACTTTTTTGAATATTTATACAAGGGGGATTTGTTACAGAGGTGCCGGGCTCTTCGC‑GGG‑t < 4:312531/147‑1 (MQ=255)
gCTACAGCTGATCGCGACAGACGTGTGCTGGTCCGGTGGTCCGG‑‑TATATATACCCTAATGATTTATAAAATTTTTATGAACTAACTTTTTGGAATATTTATAGAAGGGGGATTTGTTACAGAGGTGCCGGGCTCTTCGC‑GGG‑T‑AA‑acc < 2:418380/148‑1 (MQ=255)
cAGCTGATCGCGACAGACGTGTGCTGGTCCGGTGGTCCGG‑‑TATATATACCCTAATGATTTATAAAATTTTTATGAACTAACTTTTTGGAATATTTATAGAAGGGGGATTTGTTACAGAGGTGCCGGGCTCTTCGC‑GGG‑TAAA‑CCCGCTc < 1:28553/149‑1 (MQ=255)
aTCGCGACAGACGTGTGCTGGTCCGGTGGTCCGG‑‑TATATATACCCTAATGATTTATAAAATTTTTATGAACTAACTTTTTGGAATATTTATAGAAGGGGGATTTGTTACAGAGGTGCCGGGCTCTTCGCGGGG‑T‑AA‑ACCGcggcgaca > 2:314238/1‑141 (MQ=255)
cAGACGTGTGCTGGTCCGGTGGTCCGG‑‑TATATATACCCTAATGATTTATAAAATTTTTATGAACTAACTTTTTGGAATATTTATAGAAGGGGGATTTGTTACAGAGGTGCCGGGCTCTTCGC‑GGG‑TAAA‑CCCGCTCCTACACACATGcc < 3:326483/149‑1 (MQ=255)
aGACGTGTGCTGGTCCGGTGGTCCGG‑‑TATATATACCCTAATGATTTATAAAATTTTTATGAACTAACTTTTTGGAATATTTATAGAAGGGGGATTTGTTACAGAGGTGCCGGGCTCTTCGC‑GGGTT‑AA‑ACCCCTCCTACACACAAGCCt > 7:444075/1‑149 (MQ=255)
gACGTGTGCTGGTCCGGTGGTCCGG‑‑TATATATACCCTAATGATTTATAAAATTTTTATGAACTAACTTTTTGGAATATTTATAGAAGGGGGATTTGTTACAGAGGTGCCGGGCTCTTCGC‑GGG‑TAAA‑CCCGCTCCTACACACATGCCTc < 5:218062/149‑1 (MQ=255)
cGTGTGCTGGTCCGGTGGTCCGG‑‑TATATATACCCTAATGATTTATAAAATTTTTATGAACTAACTTTTTGGAATATTTATAGAAGGGGGATTTGTTACAGAGGTGCCGGGCTCTTCGC‑GGG‑TAAA‑CCCGCTCCTACACACATGCCTCaa < 3:139527/149‑1 (MQ=255)
gtgtGCTGGTCCGGTGGTCCGG‑‑TATATATACCCTAATGATTTATAAAATTTTTATGAACTAACTTTTTGGAATATTTATAGAAGGGGGATTTGTTACAGAGGTGCCGGGCTCTTCGC‑GGG‑TAAA‑CCCGCTCCTACACACATGCCTCAAg < 3:17187/149‑1 (MQ=255)
gtgCTGGTCCGGTGGTCCGG‑‑TATATATACCCTAATGATTTATAAAATTTTTATGAACTAACTTTTTGGAATATTTATAGAAGGGGGATTTGTTACAGAGGTGCCGGGCTCTTCGC‑GGG‑TAAA‑CCCGCTCCTACACACATGCCTCAAGa > 6:44073/1‑148 (MQ=255)
tgCTGGTCCGGTGGTCCGG‑‑TATATATACCCTAATGATTTATAAAATTTTTATGAACTAACTTTTTGGAATATTTATAGAAGGGGGATTTGTTACAGAGGTGCCGGGCTCTTCGC‑GGG‑TAAA‑CCCGCTCCTACACACATGCCTCAAGATc < 5:419736/149‑1 (MQ=255)
gtccggtggtccggtaTATATATACCCTAATGATTTATAAAATTTTTATGAACTAACTTTTTGGAATATTTATAGAAGGGGGATTTGTTACAGAGGTGCCGGGCTCTTCGC‑GGG‑TAAA‑CCCGCTCCTACACACATGCCTCAAGATCtgt < 8:435710/149‑1 (MQ=255)
gtggtccgg‑‑tATATATACCCTAATGATTTATAAAATTTTTATGAACTAACTTTTTGGAATATTTATAGAAGGGGGATTTGTTACAGAGGTGCCGGGCTCTTCGC‑GGG‑TAAA‑CCCGCTCCTACACACATGCCTCAAGATCTGTGCACTg > 4:53224/1‑148 (MQ=255)
tggtccgg‑‑tATATATACCCTAATGATTTATAAAATTTTTATGAACTAACTTTTTGGAATATTTATAGAAGGGGGATTTGTTACAGAGGTGCCGGGCTCTTCGC‑GGG‑TAAA‑CCCGCTCCTACACACATGCCTCAAGATCTGTGCACTGTa < 5:44073/149‑1 (MQ=255)
tggtccgg‑‑tATATATACCCTAATGATTTATAAAATTTTTATGAACTAACTTTTTGGAATATTTATAGAAGGGGGATTTGTTACAGAGGTGCCGGGCTCTTCGC‑GGG‑TAAA‑CCCGCTCCTACACACATGCCTCAAGATCTGTGCACTGTa < 3:193044/149‑1 (MQ=255)
tggtccgg‑‑tATATATACCCTAATGATTTATAAAATTTTTATGAACTAACTTTTTGGAATATTTATAGAAGGGGGATTTGTTACAGAGGTGCCGGGCTCTTCGC‑GGG‑TAAA‑CCCGCTCCTACACACATGCCTCAAGATCTGTGCACTGTa < 8:343990/149‑1 (MQ=255)
cgg‑‑tATATATACCCTAATGATTTATAAAATTTTTATGAACTAACTTTTTGGAATATTTATAGAAGGGGGATTTGTTACAGAGGTGCCGGGCTCTTCGC‑GGG‑TAAA‑CCCGCTCCTACACACATGCCTCAAGATCTGTGCACTGTAGGAGc < 4:80763/149‑1 (MQ=255)
g‑‑tATATATACCCTAATGATTTATAAAATTTTTATGAACTAACTTTTTGGAATATTTATAGAAGGGGGATTTGTTACAGAGGTGCCGGGCTCTTCGC‑GGG‑TAAA‑CCCGCTCCTACACACATGCCTCAAGATCTGTGCACTGTAGGAGCgg < 4:97651/149‑1 (MQ=255)
tataCCCTAATGATTTATAAAATTTTTATGAACTAACTTTTTGGAATATTTATAGAAGGGGGATTTGTTACAGAGGTGCCGGGCTCTTCGC‑GGG‑TAAA‑CCCGCTCCTACACACATGCCTCAAGATCTGTGCACTGTAGGAGCGGGttt < 3:53224/148‑1 (MQ=255)
cTAATGATTTATAAAATTTTTATGAACTAACTTTTTGGAATATTTATAGAAGGGGGATTTGTTACAGAGGTGCCGGGCTCTTCGC‑GGGTT‑AA‑ACCGCTCCTACACACATGCCGCAATATGTGTGCACGGTAGGAGCGGGGTTTccccc > 6:306503/1‑146 (MQ=255)
tAATGATTTATAAAATTTTTATGAACTAACTTTTTGGAATATTTATAGAAGGGGGATTTGTTACAGAGGTGCCGGGCTCTTCGC‑GGG‑TAAA‑CCCGCTCCTACACACATGCCTCAAGATCTGTGCACTGTAGGAGCGGGTTTAc > 2:299325/1‑143 (MQ=255)
tAATGATTTATAAAATTTTTATGAACTAACTTTTTGGAATATTTATAGAAGGGGGATTTGTTACAGAGGTGCCGGGCTCTTCGC‑GGG‑TAAA‑CCCGCTCCTACACACATGCCTCAAGATCTGTGCACTGTAGGAGCGGGTTTAc < 1:299325/143‑1 (MQ=255)
gggCTCTTCGC‑GGC‑A‑AACCCCGCCCCAACACACCTCCCTCATCTTCTGTCCACTGTCGCCGGGGTTTTACCCGCGAAAGGGCCGGAACAGGTTTACTCGGAGGCCGCAGTCCCGAGGAACTTGCGCAAGAACTGCCGCGTACGCTcttc < 6:224527/149‑1 (MQ=255)
|
ATGTCGCTACAGCTGATCGCGACAGACGTGTGCTGGTCCGGTGGTCCGG‑‑TATATATACCCTAATGATTTATAAAATTTTTATGAACTAACTTTTTGGAATATTTATAGAAGGGGGATTTGTTACAGAGGTGCCGGGCTCTTCGC‑GGG‑T‑AA‑CCCGCTCCTACACACATGCCTCAAGATCTGTGCACTGTAGGAGCGGGTTTACCCGCGAAAGGGCCGGAACAGGTTTACTCGGAGGCCGCAGTCCCGAGGAACTTGCGCAAGAACTGCCGCGTACGCTCTTC > NC_002947_CJ‑RC/278595‑278875
|
| 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
CGCTACAGCTGATCGCGACAGACGTGTGCTGGTCCGGTGGTCCGGTATATATACCCTAATGATTTATAAAATTTTTATGAACTAACTTTTTGGAATATTTATAGAAGGGGGATTTGTTACAGAGGTGCCGGGCTCTTCGCGGG‑‑‑T‑‑AACCCGCTCCTACACACATGCCTCAAGATCTGTGCACTGTAGGAGCGGGTTTACCCGCGAAAGGGCCGGAACAGGTTTACTCGGAGGCCGCAGTCCCGAGGAACTTGCGCAAGAACTGCCGCGTACGCTCTTCCTTCGGCGCTGCAAAC > NC_002947_CJ‑RC/278599‑278891
|
CGCTACAGCTGATCGCGACAGACGTGTGCTGGTCCGGTGGTCCGGTATATATACCCTAATGATTTATAAAATTTTTATGAACTAACTTTTTGGAATATTTATAGAAGGGGGATTTGTTACAGAGGTGCCGGGCTCTTCGCGGGGGTT‑‑AACC > NB501016:282:H2V7GAFX2:3:11403:14332:7142/1‑151 (MQ=60)
ACAGCTGATCGCGACAGACGTGTGCTGGTCCGGTGGTCCGGTATATATACCCTAATGATTTATAAAATTTTTATGAACTAACTTTTTGGAATATTTATAGAAGGGGGATTTGTTACAGAGGTGCCGGGCTCTTCGCGGG‑‑‑TA‑AACCCGCTCC < NB501016:282:H2V7GAFX2:1:11105:4756:7257/151‑1 (MQ=60)
ACAGACGTGTGCTGGTCCGGTGGTCCGGTATATATACCCTAATGATTTATAAAATTTTTATGAACTAACTTTTTGGAATATTTATAGAAGGGGGATTTGTTACAGAGGTGCCGGGCTCTTCGCGGG‑‑‑TA‑AACCCGCTCCTACACACATGCCT < NB501016:282:H2V7GAFX2:2:21208:19167:9824/151‑1 (MQ=60)
CAGACGTGTGCTGGTCCGGTGGTCCGGTATATATACCCTAATGATTTATAAAATTTTTATGAACTAACTTTTTGGAATATTTATAGAAGGGGGATTTGTTACAGAGGTGCCGGGCTCTTCGCGGG‑‑‑TTAAACCC‑CTCCTACACACAAGCCTC > NB501016:282:H2V7GAFX2:4:21610:16897:17934/1‑151 (MQ=60)
AGACGTGTGCTGGTCCGGTGGTCCGGTATATATACCCTAATGATTTATAAAATTTTTATGAACTAACTTTTTGGAATATTTATAGAAGGGGGATTTGTTACAGAGGTGCCGGGCTCTTCGCGGG‑‑‑TA‑AACCCGCTCCTACACACATGCCTCA < NB501016:282:H2V7GAFX2:3:11611:26050:20065/151‑1 (MQ=60)
ACGTGTGCTGGTCCGGTGGTCCGGTATATATACCCTAATGATTTATAAAATTTTTATGAACTAACTTTTTGGAATATTTATAGAAGGGGGATTTGTTACAGAGGTGCCGGGCTCTTCGCGGG‑‑‑TA‑AACCCGCTCCTACACACATGCCTCAAG < NB501016:282:H2V7GAFX2:2:11211:4497:19518/151‑1 (MQ=60)
CGTGTGCTGGTCCGGTGGTCCGGTATATATACCCTAATGATTTATAAAATTTTTATGAACTAACTTTTTGGAATATTTATAGAAGGGGGATTTGTTACAGAGGTGCCGGGCTCTTCGCGGG‑‑‑TA‑AACCCGCTCCTACACACATGCCTCAAGA < NB501016:282:H2V7GAFX2:2:11103:15174:18555/151‑1 (MQ=60)
GTGCTGGTCCGGTGGTCCGGTATATATACCCTAATGATTTATAAAATTTTTATGAACTAACTTTTTGGAATATTTATAGAAGGGGGATTTGTTACAGAGGTGCCGGGCTCTTCGCGGG‑‑‑TA‑AACCCGCTCCTACACACATGCCTCAAGATCT < NB501016:282:H2V7GAFX2:3:21609:17599:11740/151‑1 (MQ=60)
GTGGTCCGGTATATATACCCTAATGATTTATAAAATTTTTATGAACTAACTTTTTGGAATATTTATAGAAGGGGGATTTGTTACAGAGGTGCCGGGCTCTTCGCGGG‑‑‑TA‑AACCCGCTCCTACACACATGCCTCAAGATCTGTGCACTGTAG < NB501016:282:H2V7GAFX2:2:11308:1945:7424/151‑1 (MQ=60)
GTGGTCCGGTATATATACCCTAATGATTTATAAAATTTTTATGAACTAACTTTTTGGAATATTTATAGAAGGGGGATTTGTTACAGAGGTGCCGGGCTCTTCGCGGG‑‑‑TA‑AACCCGCTCCTACACACATGCCTCAAGATCTGTGCACTGTAG < NB501016:282:H2V7GAFX2:3:11408:3463:6813/151‑1 (MQ=60)
ATATACCCTAATGATTTATAAAATTTTTATGAACTAACTTTTTGGAATATTTATAGAAGGGGGATTTGTTACAGAGGTGCCGGGCTCTTCGCGGG‑‑‑TA‑AACCCGCTCCTACACACATGCCTCAAGATCTGTGCACTGTAGGAGCGGGTTTA < NB501016:282:H2V7GAFX2:2:11109:25649:18700/150‑1 (MQ=60)
CTAATGATTTATAAAATTTTTATGAACTAACTTTTTGGAATATTTATAGAAGGGGGATTTGTTACAGAGGTGCCGGGCTCTTCGCGGG‑‑‑TA‑AACCCGCTCCTACACACATGCCTCAAGATCTGTGCACTGTAGGAGCGGGTTTACA < NB501016:282:H2V7GAFX2:1:21201:20587:4660/145‑1 (MQ=60)
CGGG‑‑‑TA‑AACCCGCTCCTACACACATGCCTCAAGATCTGTGCACTGTAGGAGCGGGTTTACCCGCGAAAGGGCCGGAACAGGTTTACTCGGAGGCCGCAGTCCCGAGGAACTTGCGCAAGAACTGCCGCGTACGCTCTTCCTTCGGCGCTGC > NB501016:282:H2V7GAFX2:1:11301:16705:17776/1‑151 (MQ=60)
taAACCCGCTCCTACACACATGCCTCAAGATCTGTGCACTGTAGGAGCGGGTTTACCCGCGAAAGGGCCGGAACAGGTTTACTCGGAGGCCGCAGTCCCGAGGAACTTGCGCAAGAACTGCCGCGTACGCTCTTCCTTCGGCGCTGCAAAC > NB501016:282:H2V7GAFX2:2:21203:24205:13588/3‑151 (MQ=60)
AACCCGCTCCTACACACATGCCTCAAGATCTGTGCACTGTAGGAGCGGGTTTACCCGCGAAAGGGCCGGAACAGGTTTACTCGGAGGCCGCAGTCCCGAGGAACTTGCGCAAGAACTGCCGCGTACGCTCTTCCTTCGGCGCTGCAAAC > NB501016:282:H2V7GAFX2:2:21102:24453:5340/1‑149 (MQ=60)
ACCCGCTCCTACACACATGCCTCAAGATCTGTGCACTGTAGGAGCGGGTTTACCCGCGAAAGGGCCGGAACAGGTTTACTCGGAGGCCGCAGTCCCGAGGAACTTGCGCAAGAACTGCCGCGTACGCTCTTCCTTCGGCGCTGCAAAC < NB501016:282:H2V7GAFX2:1:11306:1639:5918/148‑1 (MQ=60)
|
CGCTACAGCTGATCGCGACAGACGTGTGCTGGTCCGGTGGTCCGGTATATATACCCTAATGATTTATAAAATTTTTATGAACTAACTTTTTGGAATATTTATAGAAGGGGGATTTGTTACAGAGGTGCCGGGCTCTTCGCGGG‑‑‑T‑‑AACCCGCTCCTACACACATGCCTCAAGATCTGTGCACTGTAGGAGCGGGTTTACCCGCGAAAGGGCCGGAACAGGTTTACTCGGAGGCCGCAGTCCCGAGGAACTTGCGCAAGAACTGCCGCGTACGCTCTTCCTTCGGCGCTGCAAAC > NC_002947_CJ‑RC/278599‑278891
|
| Alignment Legend |
|---|
Aligned base mismatch/match (shaded by quality score): ATCG/ATCG < 0 ≤ ATCG/ATCG < 14 ≤ ATCG/ATCG < 27 ≤ ATCG/ATCG < 36 ≤ ATCG/ATCG |
Unaligned base: atcg Masked matching base: atcg Alignment gap: ‑ Deleted base: ‑ |
