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 |
|
A3 F14 I1 R1
|
57 |
58.2 |
2652386 |
98.6% |
2615252 |
146.9 |
Breseq alignment
BRESEQ :: Evidence
|
| evidence |
seq id |
position |
mutation |
annotation |
gene |
description |
| RA |
NC_002947_CJ‑RC |
5,558,423 |
+GCC |
intergenic (‑84/+87) |
PP_4887 ← / ← PP_4888 |
hypothetical protein/methyl‑accepting chemotaxis transducer |
|
| |
seq id |
position |
ref |
new |
freq |
score (cons/poly) |
reads |
annotation |
genes |
product |
| * | NC_002947_CJ‑RC | 5,558,423 | 1 | . | G | 88.2%
| 34.4
/ ‑3.0
| 19 | intergenic (‑84/+87) | PP_4887/PP_4888 | hypothetical protein/methyl‑accepting chemotaxis transducer |
| Reads supporting (aligned to +/- strand): ref base . (0/2); major base G (6/9); minor base C (0/2); total (6/13) |
| Fisher's exact test for biased strand distribution p-value = 5.15e-01 |
| Kolmogorov-Smirnov test that lower quality scores support variant p-value = 1.00e+00 |
| * | NC_002947_CJ‑RC | 5,558,423 | 2 | . | C | 89.5%
| 57.3
/ 0.5
| 19 | intergenic (‑84/+87) | PP_4887/PP_4888 | hypothetical protein/methyl‑accepting chemotaxis transducer |
| Reads supporting (aligned to +/- strand): ref base . (0/2); new base C (6/11); total (6/13) |
| Fisher's exact test for biased strand distribution p-value = 1.00e+00 |
| Kolmogorov-Smirnov test that lower quality scores support variant p-value = 9.88e-01 |
| * | NC_002947_CJ‑RC | 5,558,423 | 3 | . | C | 84.2%
| 53.8
/ 4.3
| 19 | intergenic (‑84/+87) | PP_4887/PP_4888 | hypothetical protein/methyl‑accepting chemotaxis transducer |
| Reads supporting (aligned to +/- strand): ref base . (0/3); new base C (6/10); total (6/13) |
| Fisher's exact test for biased strand distribution p-value = 5.17e-01 |
| Kolmogorov-Smirnov test that lower quality scores support variant p-value = 9.80e-01 |
TCACTGTGCAGGAAATTCAGGTCGGCCTGGGCAGCGATTAGTCGGGCGGACATGAGCAACTCCTTTTGTCATGTGTCGCCGACAGCATAGCAACACCGCTCAGGTGTGGGAGCGGCCTT‑GTGTCGCGAAAGGGCCGCATA‑‑‑G‑CG‑‑‑CCGGC‑AATTTCCGCGTGTATGCAACAAACCTGGGGCTGCTATGCAGCCCTTTCGCGACACAAGGCCCACAAAGGACCGCGCAGGCTTCAGGCCCGGAACTGGCCCAGGCTGGCGCGCAGCTGAGCCGC > NC_002947_CJ‑RC/5558281‑5558551
|||
tCACTGTGCAGGAAATTCAGGTCGGCCTGGGCAGCGATTAGTCGGGCGGACATGAGCAACTCCTTTTGTCATGTGTCGCCGACAGCATAGCAACACCGCTCAGGTGTGGGAGCGGCCTT‑GTGTCGCGAAAGGGCCGCATA‑‑‑g‑cggccccg < 2:88820/149‑7 (MQ=255)
aaTTCCGGTCGGCCTGGGCAGCGATTAGTCGGGCGGACATGAGCAACTCCTTTTGTCATGTGTCGCCGACAGCATAGCAACCCCGCTCAGGTGTGGGAGCGGCCTT‑GTGTCGCTAAAGGGCCGAATA‑‑‑G‑CGGCCCCGGC‑AATTTCCGCgt < 8:200909/149‑1 (MQ=38)
aaTTCAGGTCGGCCTGGGCAGCGATTTGTCGGGCGGACATGAGCAACTCCTTTTGTCATGTGTCGCCGACAGCATAGCAACACCGCTCAGGGGTGGGAGCGGCCTT‑GTGGCGCTAAAGGGCCGCTTAGGGG‑CC‑‑‑CCGGC‑AATTTCCGCgt < 8:200582/149‑1 (MQ=255)
aGGTCGGCCTGGGCAGCTATTAGTCGGGCGGACATGAGCAACTCCTTTTGTCATGTGTCGCCCACAGCATACCAACACCGCTCAGGTGTGGGAGCGGCCTT‑GTGTCGCTAAAGGGCCGCATA‑‑‑G‑CGGCCCCGGC‑AATTTCCGCGTGTATg < 8:174103/149‑1 (MQ=37)
ggTCGGCCTGGGCAGCGATTAGTCGGGCGGACATGAGCAACTCCTTTTGTCATGTGTCGCCGACAGCATAGCAACACCGCTCAGGTGTGGGAGCGGCCTT‑GTGTCGCGAAAGGGCCGCATA‑‑‑G‑CGGCCCCGGC‑AATTTCCGCGTGTATg > 7:226778/1‑148 (MQ=255)
aGCGATTAGGCGGGCGCACATGAGCAACTCCTTTTGACTTGTGGCGCCGACAGCATCCCACCACCCCTCAGGTGTGGGAGCGGCCTT‑GGGCCGCCAACGGGCCGCATA‑‑‑G‑CGCCCCCGGC‑AATTTCCGCGTGTATGCAACAAACCTgggg < 7:340804/149‑1 (MQ=255)
ggcGGGCGGACATGAGCAACTCCTTTTTTCTTGTGTCGCCGAAAGCATACCAACACCGCTCCGGTGTGGGAGCGGCGTT‑GTGTCGCGAAAGGGCCGCATA‑‑‑G‑CGGCCCCGGC‑AATTTCCGCGTGTATGCAACAAACCTGGGGCTGCTAt < 4:31138/146‑1 (MQ=37)
aattcctcAACTCCTTTTTTATTTTGTCCCCTCCAGCATCGATACCCGGGTCTGGTG‑GGGGCCGGCCTTGGTGTCTCTAACGGGCCTCATA‑‑‑G‑CGCCCCCGGC‑TATTTCCGCGTGTATGCAACAAACCTGGGGCTGCTATGCAGCCCtt < 2:245066/141‑1 (MQ=255)
aTGAGCAACTCCTTTTGTCATGTGTCGCCGACAGCATAGCAACACCGCTCAGGTGTGGGAGCGGCCTT‑GTGTCGCTAAAGGGCCGCATA‑‑‑G‑CGGCCCCGGC‑AATTTCCGCGTGTATGCAACAAACCTGGGGCTGCTATGCAGCCCTTTcg < 5:131098/149‑1 (MQ=38)
aTGAGCAACTCCTTTTGTCATGTGTCGCCGACAGCATAGCAACACCGCTCAGGTGTGGGAGCGGCCTT‑GTGTCGCGAAAGGGCCGCATA‑‑‑G‑CGGCCCCGGC‑AATTTCCGCGTGTATGCAACAAACCTGGGGCTGCTATGCAGCCCTTTcg < 8:226778/149‑1 (MQ=255)
tGAGCAACTCCTTTTGTCATGTGTCGCCGACAGCATAGCAACACCGCTCAGGTGTGGGAGCGGCCTT‑GTGTCGCGAAAGGGCCGCATA‑‑‑G‑CGGCCCCGGC‑AATTTCCGCGTGTATGCAACAAACCTGGGGCTGCTATGCAGCCCTTTcgc < 2:261945/149‑1 (MQ=255)
aaCTCCTTTTGTCATGTGTCGCCGACAGCATAGCAACACCGCTCAGGTGTGGGAGCGGCCTT‑GTGTCGCTAAAGGGCCGCATA‑‑‑G‑CGGCCCCGGC‑AATTTCCGCGTGTATGCAACAAACCTGGGGCTGCTATGCAGCCCTTTCGCGacac < 8:45301/149‑1 (MQ=38)
ccGCTCCGTTGTGGTAGCGGCTTT‑GTGCCCCTAACGGCCCCAAAA‑‑‑G‑CGGC‑CCCGCAAATTACCGCGTGTATGCAACAAACCTGGGGCTGCTATGCAGCCCTTTCGCTACACAAGGCCCACAAAGGACCGCGCAGGCTTCAGGCCCGGaa < 6:252547/149‑1 (MQ=255)
tgGGTGCGGCCTT‑GTGCCGCCAATGGGCCGCATACG‑GCCC‑‑‑CCGGC‑AATTTCCGCGTTTATGCAACAAACCTGGGGCTGCTATGCAGCCCTTTCGCGACACAAGGCCCACAAAGGACCGCGCAGGCTTCAGGCCCGGAACTGGCCCAgg < 6:135625/148‑1 (MQ=37)
ccTT‑GTGTGGCGAAAGGGCCGCATA‑‑‑G‑CGGCCCCGGC‑AATTTCCGCGTGTATGCAACAAACCTGGGGCTGCTATGCAGCCCTTTCGCGAAACAAGGCCCACAAAGGACCGCGCAGGCTTCAGGCCCGGAACTGGCCCAGGCTGGCGCGCa < 2:203042/149‑1 (MQ=255)
tt‑GTGTCGCGAAAGGGCCGCATA‑‑‑G‑CGGCCCCGGC‑AATTTCCGCGTGTATGCAACAAACCTGGGGCTGCTATGCAGCCCTTTCGCGACACAAGGCCCACAAAGGACCGCGCAGGCTTCAGGCCCGGAACTGGCCCAGGCTGGCGCGCAGc > 6:78963/1‑149 (MQ=255)
tt‑GTGTCGCGAAAGGGCCGCATA‑‑‑G‑CGGCCCCGGC‑AATTTCCGCGTGTATGCAACAAACCTGGGGCTGCTATGCAGCCCTTTCGCGACACAAGGCCCACAAAGGACCGCGCAGGCTTCAGGCCCGGAACTGGCCCAGGCTGGCGCGCAGc > 4:62956/1‑149 (MQ=255)
tt‑GTGTCGCGAAAGGGCCGCATA‑‑‑G‑CGGCCCCGGC‑AATTTCCGCGTGTATGCAACAAACCTGGGGCTGCTATGCAGCCCTTTCGCGACACAAGGCCCACAAAGGACCGCGCAGGCTTCAGGCCCGGAACTGGCCCAGGCTGGCGCGCAGc > 4:58316/1‑149 (MQ=255)
gtgtCGCGAAAGGGCCGCATA‑‑‑G‑CGGCCCCGGC‑AATTTCCGCGTGTATGCAACAAACCTGGGGCTGCTATGCAGCCCTTTCGCGACACAAGGCCCACAAAGGACCGCGCAGGCTTCAGGCCCGGAACTGGCCCAGGCTGGCGCGCAGCTg > 7:110057/1‑149 (MQ=255)
aaaGGGCCGCATA‑‑‑G‑CGGCCCCGGC‑AATTTCCGCGTGTATGCAACAAACCTGGGGCTGCTATGCAGCCCTTTCGCGACACAAGGCCCACAAAGGACCGCGCAGGCTTCAGGCCCGGAACTGGCCCAGGCTGGCGCGCAGCTGAgccgc > 2:229603/1‑147 (MQ=255)
|||
TCACTGTGCAGGAAATTCAGGTCGGCCTGGGCAGCGATTAGTCGGGCGGACATGAGCAACTCCTTTTGTCATGTGTCGCCGACAGCATAGCAACACCGCTCAGGTGTGGGAGCGGCCTT‑GTGTCGCGAAAGGGCCGCATA‑‑‑G‑CG‑‑‑CCGGC‑AATTTCCGCGTGTATGCAACAAACCTGGGGCTGCTATGCAGCCCTTTCGCGACACAAGGCCCACAAAGGACCGCGCAGGCTTCAGGCCCGGAACTGGCCCAGGCTGGCGCGCAGCTGAGCCGC > NC_002947_CJ‑RC/5558281‑5558551
|
| Alignment Legend |
|---|
Aligned base mismatch/match (shaded by quality score): ATCG/ATCG < 3 ≤ 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: ‑ |
GATK/CNVnator alignment
N/A
