Predicted mutation
evidence	seq id	position	mutation	annotation	gene	description
JC	NC_000913	61,712	Δ11 bp	coding (1543‑1553/2907 nt)	rapA ←	RNA polymerase‑binding ATPase and RNAP recycling factor

New junction evidence
		seq id	position	reads (cov)	reads (cov)	score	skew	freq	annotation	gene	product
*	?	NC_000913	= 61711	1 (0.030)	20 (0.540)	14/120	0.6	95.4%	coding (1554/2907 nt)	rapA	RNA polymerase‑binding ATPase and RNAP recycling factor
	?	NC_000913	61723 =	1 (0.030)					coding (1542/2907 nt)	rapA	RNA polymerase‑binding ATPase and RNAP recycling factor

AACACCGCAGCGCGAATACCTTCACGTTCGCGCAGTACCTGCTCCAGTTGCAGCGCAGTGGCAGCTTTGGCGCAGATCACCAGCACTTTCTGAGAGCGATGGCTGGTCAGGTAGCCCATCA  >  NC_000913/61664‑61784                                                            |                                                              taccttcgtggaacaccgcagcgcgaataccttcacgttcgcgcagtacctgctccagtGGCAGc                                                          <  1:815230‑M2/6‑1 (MQ=255) taccttcgtggaacaccgcagcgcgaataccttcacgttcgcgcagtacctgctccagtGGCAGc                                                          <  1:266847‑M2/6‑1 (MQ=255)  accttcgtggaacaccgcagcgcgaataccttcacgttcgcgcagtacctgctccagtGGcaggt                                                         >  1:2848030‑M2/59‑63 (MQ=255)   ccttcgtggaacaccgcagcgcgaataccttcacgttcgcgcagtacctgctccagtGGCagcgg                                                        >  1:2735458‑M2/58‑63 (MQ=255)   ccttcgtggaacaccgcagcgcgaataccttcacgttcgcgcagtacctgctccagcGgcagggt                                                        >  1:1458366‑M2/58‑62 (MQ=255)    acCGCAGCGCGAATACCTTCACGTTCGCGCAGTACCTGCTCCAGTTGCAGCGCAGTGGCAGCatt                                                       >  1:2987204/1‑65 (MQ=255)     ttcgtggaacaccgcagcgcgaataccttcacgttcgcgcagtacctgctccagtGGCAGgtttt                                                      >  1:1572667‑M2/56‑64 (MQ=255)               accgcagcgcgaatcccttcacgttcgcgcagtacctgctccagtGGCAGCTTTGGCGCAGATCa                                            <  1:2975272‑M2/20‑1 (MQ=255)                  gcagcgcgaataccttcacgttcgcgcagtacctgctccagtGGCAGCGTTGGGGGAGAAGACCa                                         >  1:1256648‑M2/43‑65 (MQ=255)                  gcagcgcgaataccttcacgttcgcgcagtacctgctccagcGGCAGCGTTGGCGCAGATCACCa                                         >  1:1919619‑M2/43‑65 (MQ=255)                       gcgaataccttcacgttcgcgcagtacctgctccagtGGCAGCTTTGGCGCAGATCACCAGCACt                                    <  1:1126437‑M2/28‑1 (MQ=255)                             accttcacgttcgcgcagtacctgctccagtGGCAGGTTTGGCGGAGATCAACAGCACTTTTTga                              >  1:555442‑M2/32‑65 (MQ=255)                               cttcacgttcgcgcagtacctgctccagtGGCAGCTTTGGCGCAGATCACCAGCACTTTCTgaga                            <  1:1720911‑M2/36‑1 (MQ=255)                                ttcacgttcgcgcagtacctgctccagtGGCAGCTTTGGCGCAGATCACCAGCACTTTCTGagag                           <  1:792973‑M2/37‑1 (MQ=255)                                           gcagtacctgctccagtGGCAGCTTTGGCGCAGATCACCAGCACTTTCTGAGAGCGATGGCTGGt                <  1:1987102‑M2/48‑1 (MQ=255)                                              gtacctgctccagtGGCAGCTTTGGCGCAGATCACCAGCACTTTCTGAGAGCGATGGCTGGTCAg             <  1:560891‑M2/51‑1 (MQ=255)                                               tacctgctccagtGGCAGCTTTGGCGCAGATCACCAGCACTTTCTGAGAGCGATGGCTGGTCAgg            <  1:2662374‑M2/52‑1 (MQ=255)                                                tcctgctccagtGGCAGCTTTGGCGCAGATCACCAGCACTTTCTGAGAGCGATGGCTGGTCAGGt           <  1:2073919‑M2/53‑1 (MQ=255)                                                    gctccagtGGCAGCTTTGGCGCAGATCACCAGCACTTTCTGAGAGCGATGGCTGGTCAGGTAGcc       <  1:104813‑M2/57‑1 (MQ=255)                                                    gctccagtGGCAGCTTTGGCGCAGATCACCAGCACTTTCTGAGAGCGATGGCTGGGCAGGTAGcc       <  1:248460‑M2/57‑1 (MQ=255)                                                       ccagtGGCAGCTTTGGCGCAGATCACCAGCACTTTCTGAGAGCGATGGCTGGTCAGGTAGCCCAt    <  1:2827354‑M2/60‑1 (MQ=255)                                                         agtGGCAGCTTTGGCGCAGATCCCCAGCACTTTCTGAGAGCGATGGCTGGTCAGGTAGCCCATCa  <  1:937221‑M2/62‑1 (MQ=255)                                                            |                                                              AACACCGCAGCGCGAATACCTTCACGTTCGCGCAGTACCTGCTCCAGTTGCAGCGCAGTGGCAGCTTTGGCGCAGATCACCAGCACTTTCTGAGAGCGATGGCTGGTCAGGTAGCCCATCA  >  NC_000913/61664‑61784

Alignment Legend
Aligned base mismatch/match (shaded by quality score): ATCG/ATCG < 3 ≤ ATCG/ATCG < 18 ≤ ATCG/ATCG < 26 ≤ ATCG/ATCG < 31 ≤ ATCG/ATCG < 34 ≤ 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.