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 I0 R1 248 61.6 2601574 98.7% 2567753 146.9

Breseq alignment

BRESEQ :: Evidence
Predicted mutation
evidence seq id position mutation freq annotation gene description
JC NC_002947_CJ‑RC 1,311,719 Δ84 bp 27.6% intergenic (‑187/+8) PP_1144 ← / ← rapA membrane protein/RNA polymerase‑associated protein RapA

New junction evidence
  seq id position reads (cov) reads (cov) score skew freq annotation gene product
* ? NC_002947_CJ‑RC = 131171813 (0.230)6 (0.110) 6/262 NT 27.6% intergenic (‑186/+92) PP_1144/rapA membrane protein/RNA polymerase‑associated protein RapA
?NC_002947_CJ‑RC 1311803 = 19 (0.350)intergenic (‑271/+7) PP_1144/rapA membrane protein/RNA polymerase‑associated protein RapA

GCTACAACCCTGTGCAGACTGTCCAGAGGCAGTATAGGAAGGAGTACTTAAGCCTTCCTGACTAATGGCACAATGATTTCTACGATTTGGTTATAACTCCAATCGCAGTGAGGAATAAATTTGGGGCCCTAATGCCTTCCTGTGGGAGCGGG‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑  >  NC_002947_CJ‑RC/1311567‑1311718
‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑gcgggGCCTGCGCTAGCCAGCCACCAGCACGCGAATGGCTTCCAGGCGCAGGGCGGCCTTCTCCAGCATTGCCAGGCCATCTTCGCGCCGCTTGCGCAGGGCGTCGATTTCGCTGTCACGCACACTTGGGTTGACCGCTTGCAATGCCAC  >  NC_002947_CJ‑RC/1311803‑1311947
                                                                                                                                                                                                                                                                                                         
GCTACAACCCTGTGCAGACTGTCCAGAGGCAGTATAGGAAGGAGTACTTAAGCCTTCCTGACTAATGGCACAATGATTTCTACGATTTGGTTATAACTCCAATCGCAGTGAGGAATAAATTTGGGGCCCTAATGCCTTCCTGTGGGAGC                                                                                                                                                      <  8:87591/149‑1
                        AGAGGCAGTATAGGAAGGAGTACTTAAGCCTTCCTGACTAATGGCACAATGATTTCTACGATTTGGTTATAACTCCAATCGCAGTGAGGAATAAATTTGGGGCCCTAATGCCTTCCTGTGGGAGCGGGGCCTGCGCTAGCCAGCCAC                                                                                                                                >  4:136344/1‑147
                                     GAAGGAGTACTTAATCCTTCCTGACTAATGGCACAATGATTTCTACGATTTGGTTATAACTCCAATCGCAGTGAGGAATAAATTTGGGGCCCTAATGCCTTCCTGTGGGAGCGGGGCCTGCGCTAGCCAGCCACCAGCACGCGAATGGC                                                                                                                 <  2:241886/149‑1
                                                                     ACAATGATTTCTACGATTTGGTTATAACTCCAATCGCAGTGAGGAATAAATTTGGGGCCCTAATGCCTTCCTGTGGGAGCGGGGCCTGCGCTAGCCAGCCACCAGCACGCGAATGGCTTCCAGGCGCAGGGCGGCCTTCTCCAGCATTG                                                                                 >  4:219704/1‑149
                                                                                                 TCCAATCGCAGTGAGGAATAAATTTGGGGCCCTAATGCCTTCCTGTGGGAGCGGGGCCTGCGCTAGCCAGCCACCAGCACGCGAATGGCTTCCAGGCGCAGGGCGGCCTTCTCCAGCATTGCCAGGCCATCTTCGCGCCGCTTGCGCAG                                                     >  1:270858/1‑149
                                                                                                        GCAGTGAGGAATAAATTTGGGGCCCTAATGCCTTCCTGTGGGAGCGGGGCCTGCGCTAGCCAGCCACCAGCACGCGAATGGCTTCCAGGCGCAGGGCGGCCTTCTCCAGCATTGCCAGGCCATCTTCGCGCCGCTTGCGCAGGGCGTC                                               <  2:270858/148‑1
                                                                                                                               CCTAATGCCTTCCTGTGGGAGCGGGGCCTGCGCTAGCCAGCCACCAGCACGCGAATGGCTTCCAGGCGCAGGGCGGCCTTCTCCAGCATTGCCAGGCCATCTTCGCGCCGCTTGCGCAGGGCGTCGATTTCGCTGTCACGCACACTTGG                       <  3:136344/149‑1
                                                                                                                                                GGAGCGGGGCCTGCGCTAGCCAGCCACCAGCACGCGAATGGCTTCCAGGCGCAGGGCGGCCTTCTCCAGCATTGCCAGGCCATCTTCGCGCCGCTTGCGCAGGGCGTCGATTTCGCTGTCACGCACACTTGGGTTGACCGCTTGCAAT       <  3:219704/148‑1
                                                                                                                                                    CGGGGCCTGCGCTAGCCAGCCACCAGCACGCGAATGGCTTCCAGGCGCAGGGCGGCCTTCTCCAGCATTGCCAGGCCATCTTCGCGCCGCTTGCGCAGGGCGTCGATTTCGCTGTCACGCACACTTGGGTTGACCGCTTGCAATGCCAC  <  7:42029/149‑1
                                                                                                                                                                                                                                                                                                         
GCTACAACCCTGTGCAGACTGTCCAGAGGCAGTATAGGAAGGAGTACTTAAGCCTTCCTGACTAATGGCACAATGATTTCTACGATTTGGTTATAACTCCAATCGCAGTGAGGAATAAATTTGGGGCCCTAATGCCTTCCTGTGGGAGCGGG‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑  >  NC_002947_CJ‑RC/1311567‑1311718
‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑gcgggGCCTGCGCTAGCCAGCCACCAGCACGCGAATGGCTTCCAGGCGCAGGGCGGCCTTCTCCAGCATTGCCAGGCCATCTTCGCGCCGCTTGCGCAGGGCGTCGATTTCGCTGTCACGCACACTTGGGTTGACCGCTTGCAATGCCAC  >  NC_002947_CJ‑RC/1311803‑1311947

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: ‑
Reads not counted as support for junction
read_name Not counted due to insufficient overlap past the breakpoint.
read_name Not counted due to not crossing MOB target site duplication.

GATK/CNVnator alignment

N/A