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 F1 I1 R1
|
152 |
24.9 |
2083062 |
91.6% |
1908084 |
109.2 |
Breseq alignment
BRESEQ :: Evidence
|
| evidence |
seq id |
position |
mutation |
annotation |
gene |
description |
| RA |
AM260479 |
2,111,023 |
+G |
coding (563/1089 nt) |
h16_A1942 → |
Hypothetical protein |
|
| |
seq id |
position |
ref |
new |
freq |
score (cons/poly) |
reads |
annotation |
genes |
product |
| * | AM260479 | 2,111,022 | 1 | . | G | 92.3%
| 40.5
/ ‑3.1
| 13 | coding (562/1089 nt) | h16_A1942 | Hypothetical protein |
| Reads supporting (aligned to +/- strand): ref base . (1/0); new base G (4/8); total (5/8) |
| Fisher's exact test for biased strand distribution p-value = 3.85e-01 |
| Kolmogorov-Smirnov test that lower quality scores support variant p-value = 1.00e+00 |
GGACCGATCGCCAGCATGATTCCTCTTCCACAAGCGCAGTTGATCGGGCGCATCGCCAATGTGGCCGGGCGCATGCTCGCCGACGGCGCCGACGAGTATGAGACCTTCGACGAACTGGTGGAT‑GACTCGACG‑A‑GATGCGATCGACGCCGCCGCGCCGGTGCTGGCCGGCATGGTGCTCCGCCGCGCCCTCCCCTCGGTCGCGCGCGCCGCGCCCGCCGTGCGTCGCGCCGCGGTGCGCGGCGTGGCCCAGGCGG > AM260479/2110890‑2111143
|
ggACCGATCGCCAGCATGATTCCTCTTCCACAAGCGCAGTTGATCGGGCGCATCGCCAATGTGGCCGGGCGCATGCTCGCCGACGGCGCCGACGAGTATGAGACCTTCGACGAACTGGTGGATGGACTcgacg‑a < 2:442531/134‑1 (MQ=255)
aTCGCCAGCATGATTCCTCTTCCACAAGCGCAGTTGATCGGGCGCATCGCCAATGTGGCCGGGCGCATGCTCGCCGACGGCGCCGACGAGTATGAGACCTTCGACGAACTGGTGGATGGACTCGACg‑a‑ggatgc > 2:194416/1‑129 (MQ=255)
aaGCGCAGTTGATCGGGCGCATCGCCAATGTGGCCGGGCGCATGCTCGCCGACGGCGCCGACGAGTATGAGACCTTCGACGAACTGGTGGATGGACTCGACG‑AGGATGCGATCGACGCCGCCGCGCCGGTGCTg < 1:376689/134‑1 (MQ=255)
cgcAGTTGATCGGGCGCATCGCCAATGTGGCCGGGCGCATGCTCGCCGACGGCGCCGACGAGTATGAGACCTTCGACGAACTGGTGGATGGACTCGACG‑AGGATGCGATCGACGCcgccgcg < 1:291255/122‑1 (MQ=255)
cgcAGTTGATCGGGCGCATCGCCAATGTGGCCGGGCGCATGCTCGCCGACGGCGCCGACGAGTATGAGACCTTCGACGAACTGGTGGATGGACTCGACG‑AGGATGCGATCGACGCcgccgcg > 2:291255/1‑122 (MQ=255)
gggCGCATCGCCAATGTGGCCGGGCGCATGCTCGCCGACGGCGCCGACGAGTATGAGACCTTCGACGAACTGGTGGATGGACTCGACG‑AGGATGCGATCGACGCCGCCGCGCCGGTGCTGGCCGGCATGGTGc < 2:295076/133‑1 (MQ=255)
gcgcATGCTCGCCGACGGCGCCGACGAGTATGAGACCTTCGACGAACTGGTGGATGGACTCGACGAA‑GATGCGATCGACGCCGCCGCGCCGGTGCTGGCCGGCATCGCACTCCGCCCCGCCCCCCCCTCGGTcg > 2:758152/1‑134 (MQ=255)
gCCGACGGCGCCGACGAGTATGAGACCTTCGACGAACTGGTGGATGGACTCGACG‑AGGATGCGATCGACGCCGCCGCGCCGGTGCTGGCCGGCATGGTGCTCCGCCGCGCCCTCCCCTCGGTCGCGcgcgcc < 1:419459/132‑1 (MQ=255)
aCGGCGCCGACGAGTATGAGACCTTCGACGAACTGGTGGATGGACTCGACG‑AGGATGCGATCGAcg < 1:110601/66‑1 (MQ=255)
aCGGCGCCGACGAGTATGAGACCTTCGACGAACTGGTGGATGGACTCGACG‑AGGATGCGATCGAcg > 2:110601/1‑66 (MQ=255)
aCGGCGCCGACGAGTATGAGACCTTCGACGAACTGGTGGATGGACTCGACG‑AGGATGCGATCGACGCCGCCGCGCCGGTGCTGGCCGGCAt > 1:391197/1‑91 (MQ=255)
aCGGCGCCGACGAGTATGAGACCTTCGACGAACTGGTGGATGGACTCGACG‑AGGATGCGATCGACGCCGCCGCGCCGGTGCTGGCCGGCAt < 2:391197/91‑1 (MQ=255)
tggACTCGACG‑AGGATGCGATCGACGCCGCCGCGCCGGTGCTGGCCGGCATGGTGCTCCGCCGCGCCCTCCCCTCGGTCGCGCGCGCCGCGCCCGCCGTGCGTCGCGCCGCGGTGCGCGGCGTGGCCCAGGCgg < 1:194416/132‑1 (MQ=255)
tCGACG‑AGGATGCGATCGACGCCGCCGCGCCGGTGCTGGCCGGCATGGTGCTCCGCCGCGCCCTCCCCTCGGTCGCGCGCGCCGCGCccgccg < 1:511998/93‑1 (MQ=255)
tCGACG‑AGGATGCGATCGACGCCGCCGCGCCGGTGCTGGCCGGCATGGTGCTCCGCCGCGCCCTCCCCTCGGTCGCGCGCGCCGCGCccgccg > 2:511998/1‑93 (MQ=255)
|
GGACCGATCGCCAGCATGATTCCTCTTCCACAAGCGCAGTTGATCGGGCGCATCGCCAATGTGGCCGGGCGCATGCTCGCCGACGGCGCCGACGAGTATGAGACCTTCGACGAACTGGTGGAT‑GACTCGACG‑A‑GATGCGATCGACGCCGCCGCGCCGGTGCTGGCCGGCATGGTGCTCCGCCGCGCCCTCCCCTCGGTCGCGCGCGCCGCGCCCGCCGTGCGTCGCGCCGCGGTGCGCGGCGTGGCCCAGGCGG > AM260479/2110890‑2111143
|
| Alignment Legend |
|---|
Aligned base mismatch/match (shaded by quality score): ATCG/ATCG < 3 ≤ ATCG/ATCG < 16 ≤ ATCG/ATCG < 35 ≤ ATCG/ATCG < 39 ≤ ATCG/ATCG < 40 ≤ ATCG/ATCG |
Unaligned base: atcg Masked matching base: atcg Alignment gap: ‑ Deleted base: ‑ |
GATK/CNVnator alignment
BRESEQ :: bam2aln output
GCCGCGCGTGTGGTGGGACCGATCGCCAGCATGATTCCTCTTCCACAAGCGCAGTTGATCGGGCGCATCGCCAATGTGGCCGGGCGCATGCTCGCCGACGGCGCCGACGAGTATGAGACCTTCGACGAACTGGTGGAT‑GACTCGACGA‑GATGCGATCGACGCCGCCGCGCCGGTGCTGGCCGGCATGGTGCTCCGCCGCGCCCTCCCCTCGGTCGCGCGCGCCGCGCCCGCCGTGCGTCGCGCCGCGGTGCGCGGCGTGGCCCAGGCGGTGCGAACGGCCACCCGCACCAGC > AM260479/2110875‑2111166
|
GCCGCGCGTGTGGTGGGACCGATCGCCAGCATGATTCCTCTTCCACAAGCGCAGTTGATCGGGCGCATCGCCAATGTGGCCGGGCGCATGCTCGCCGACGGCGCCGACGAGTATGAGACCTTCGACGAACTGGTGGATGGACTCGACGA‑G < GWNJ‑0478:712:GW2002102894th:2:1210:11214:73206/150‑1 (MQ=60)
ggcatacgagatgtagctccgtctcgtgggctcggagatgtgtataagagacaGGGCGCATGCTCGCCGACGGCGCCGACGAGTATGAGACCTTCGACGAACTGGTGGATGGACTCGACGAGGATGCGATCGACGCCGCCGCGCCGGTGC < GWNJ‑0478:712:GW2002102894th:2:1108:9301:47007/97‑1 (MQ=60)
CCTCTTCCACAAGCGCAGTTGATCGGGCGCATCGCCAATGTGGCCGGGCGCATGCTCGCCGACGGCGCCGACGAGTATGAGACCTTCGACGAACTGGTGGATGGACTCGACGAGGATGCGATCGACGCCGCCGCGCCGGTGCTGGCCctg < GWNJ‑0478:712:GW2002102894th:2:1202:6190:37919/150‑4 (MQ=60)
CAAGCGCAGTTGATCGGGCGCATCGCCAATGTGGCCGGGCGCATGCTCGCCGACGGCGCCGACGAGTATGAGACCTTCGACGAACTGGTGGATGGACTCGACGAGGATGCGATCGACGCCGCCGCGCCGGTGCTGGCCGGCATGGTGCTC < GWNJ‑0478:712:GW2002102894th:2:1208:13310:88168/150‑1 (MQ=60)
GGCGCATGCTCGCCGACGGCGCCGACGAGTATGAGACCTTCGACGAACTGGTGGATGGACTCGACGAGGATGCGATCGACGCCGCCGCGCCGGTGCTGGCCGGCATGGTGCTCCGCCGCGCCtgtctcttatacacatctccgagcccac > GWNJ‑0478:712:GW2002102894th:2:1209:3197:77544/1‑122 (MQ=60)
CGCCGACGGCGCCGACGAGTATGAGACCTTCGACGAACTGGTGGATGGACTCGACGAGGATGCGATCGACGCCGCCGCGCCGGTGCTGGCCGGCATGGTGCTCCGCCGCGCCCTCCCCTCGGTCGCGCGCGCCGCGCCCGCCGTGCGT < GWNJ‑0478:712:GW2002102894th:2:1210:14987:37195/148‑1 (MQ=60)
gggctcggagatgtgtataagagacaGAACTGGTGGATGGACTCGACGAGGATGCGATCGACGCCGCCGCGCCGGTGCTGGCCGGCATGGTGCTCCGCCGCGCCCTCCCCTCGGTCGCGCGCGCCGCGCCCGCCGTGCGTCGCGCCGCGG < GWNJ‑0478:712:GW2002102894th:2:1216:17141:32674/124‑1 (MQ=60)
GTATGAGACCTTCGACGAACTGGTGGATGGACTCGACGA‑Ggactgtctcttatacacatctccgagcccacgagacggagctacatctcgtatgccgtcttctgcttgaaaaaaaaaaaaaaaaagagaagaaaaaagtaaagaattaac > GWNJ‑0478:712:GW2002102894th:2:2211:14948:70287/1‑40 (MQ=60)
atgGACTCGACGAGGATGCGATCGACGCCGCCGCGCCGGTGCTGGCCGGCATGGTGCTCCGCCGCGCCCTCCCCTCGGTCGCGCGCGCCGCGCCCGCCGTGCGTCGCGCCGCGGTGCGCGGCGTGGCCCAGGCGGTGCGAACGGCCACCC < GWNJ‑0478:712:GW2002102894th:2:1112:16412:42165/147‑1 (MQ=60)
G‑GACTCGACGAGGATGCGATCGACGCCGCCGCGCCGGTGCTGGCCGGCATGGTGCTCCGCCGCGCCCTCCCCTCGGTCGCGCGCGCCGCGCCCGCCGTGCGTCGCGCCGCGGTGCGCGGCGTGGCCCAGGCGGTGCGAACGGCCACCCGC > GWNJ‑0478:712:GW2002102894th:2:2215:19021:37473/1‑150 (MQ=60)
ACGAGGATGCGATCGACGCCGCCGCGCCGGTGCTGGCCGGCATGGTGCTCCGCCGCGCCCTCCCCTCGGTCGCGCGCGCCGCGCCCGCCGTGCGTCGCGCCGCGGTGCGCGGCGcgcgcgacctgtctcttatacacatctccgagccc > GWNJ‑0478:712:GW2002102894th:2:1114:4188:39228/1‑114 (MQ=60)
|
GCCGCGCGTGTGGTGGGACCGATCGCCAGCATGATTCCTCTTCCACAAGCGCAGTTGATCGGGCGCATCGCCAATGTGGCCGGGCGCATGCTCGCCGACGGCGCCGACGAGTATGAGACCTTCGACGAACTGGTGGAT‑GACTCGACGA‑GATGCGATCGACGCCGCCGCGCCGGTGCTGGCCGGCATGGTGCTCCGCCGCGCCCTCCCCTCGGTCGCGCGCGCCGCGCCCGCCGTGCGTCGCGCCGCGGTGCGCGGCGTGGCCCAGGCGGTGCGAACGGCCACCCGCACCAGC > AM260479/2110875‑2111166
|
| Alignment Legend |
|---|
Aligned base mismatch/match (shaded by quality score): ATCG/ATCG < 0 ≤ ATCG/ATCG < 30 ≤ ATCG/ATCG < 35 ≤ ATCG/ATCG < 39 ≤ ATCG/ATCG < 40 ≤ ATCG/ATCG |
Unaligned base: atcg Masked matching base: atcg Alignment gap: ‑ Deleted base: ‑ |
