Predicted mutation
evidence	seq id	position	mutation	annotation	gene	description
JC JC	NC_000913	3,720,136	IS3 (–) +3 bp	coding (88‑90/213 nt)	cspA →	cold shock protein CspA

New junction evidence
		seq id	position	reads (cov)	reads (cov)	score	skew	freq	annotation	gene	product
*	?	NC_000913	2170171 =	NA (NA)	25 (0.740)	25/484	0.4	96.1%	noncoding (1/1258 nt)	IS3	repeat region
	?	NC_000913	3720136 =	1 (0.030)					coding (88/213 nt)	cspA	cold shock protein CspA
*	?	NC_000913	= 2171428	NA (NA)	35 (1.040)	35/484	0.1	97.2%	noncoding (1258/1258 nt)	IS3	repeat region
	?	NC_000913	= 3720138	1 (0.030)					coding (90/213 nt)	cspA	cold shock protein CspA

AGTATGAGCGCAAAAGGTTGCTGCTACGATAATGCCTGCGTGGAAAGCTTCTTTCATTCGCTGAAAGTGGAATGTATCCATGGAGAACACTTTATCAGCCGGGAAATAATGCGGGCAACGGTGTTTAATTATATCGAATGTGATTACAATCGGTGGCGGCGGCACAGTTGGTGTGGCGGCCTCAGTCCGGAACAATTTGAAAACAAGAACCTCGCTTAGGCCTGTGTCCATATTACGTGGGTAGGATCAGTCATCCCTTCGTGGATCATTTTGACTGCCGCCTGCGCTATTCTGTTTTTTGGCGCGCTGGCGAGCTGAAATCGCTCTTTAAACCCGACTTCCTGGGTCTCGGTTTCACTATTACCAGACATTATTTTCGCCGCACCGCCATGAAAGCGCGTAACCACGCCTTTTTGTTCGAGAAAGCGCAAATCGGCACGGATTGTCGCTTCCGAGGCAGCAAATACTCCCGCCAGATCCTGAACAAGCACGGTTCCCT  >  NC_000913/2171180‑2171678                                                                                                                                                                                                                                                         |                                                                                                                                                                                                                                                           aGTATGAGCGCAAAAGGTTGCTGCTACGATAATGCCTGCGTGGAAAGCTTCTTTCATTCGCTGAAAGTGGAATGTATCCATGGAGAACACTTTATCAGCCGGGAAATAATGCGGGCAACGGTGTTTAATTATATCGAATGTGATTACAATCGGTGGCGGCGGCACAGTTGGTGTGGCGGCCTCAGTCCGGAACAATTTGAAAACAAGAACCTCGCTTAGGCCCGTGTCCATATTTCGTGGGGAGGATCAGt                                                                                                                                                                                                                                                          >  2:73498/1‑251 (MQ=11)                          aCGATAATGCCTGCGTGGAAAGCTTCTTTCATTCGCTGAAAGTGGAATGTATCCATGGAGAACACTTTATCAGCCGGGAAATAATGCGGGCAACGGTGTTTAATTATATCGAATGTGATTACAATCGGTGGCGGCGGCACAGTTGGTGTGGCGGCCTCAGTCCGGAACAATTTGAAAACAAGAACCTCGCTTAGGCCTGTGTCCATATTACGTGGGTAGGATCAGTCATCCCTTCGTGGATCATTTTGACt                                                                                                                                                                                                                                 <  2:40459/251‑1 (MQ=255)                                            aaaGCTTCTTTCATTCGCTGAAAGTGGAATGTATCCATGGAGAACACTTTATCAGCCGGGAAATAATGCGGGCAACGGTGTTTAATTATATCGAATGTGATTACAATCGGTGGCGGCGGCACAGTTGGTGTGGCGGCCTCAGTCCGGAACAATTTGAAAACAAGAACCTCGCTTAGGCCTGTGTCCATATTACGTGGTTAGGATCAGTCATCCCTTCGTGGATCATTTTGACTGCCGCCTGCGCTATTCTg                                                                                                                                                                                                               <  1:27864/251‑1 (MQ=255)                                                  tcttTCATTCGCTGAAAGTGGAATGTATCCATGGAGAACACTTTATCAGCCGGGAAATAATGCGGGCAACGGTGTTTAATTATATCGAATGTGATTACAATCGGTGGCGGCGGCACAGTTGGTGTGGCGGCCTCAGTCCGGAACAATTTGAAAACAAGAACCTCGCTTAGGCCTGTGTCCATATTACGTGGGTAGGATCAGTCATCCCTTCGTGGATCATTTTGACTGCCGCCTGCGCTATTCTGttttt                                                                                                                                                                                                          <  1:283763/250‑1 (MQ=255)                                                     ttCATTCGCTGAAAGTGGAATGTATCCATGGAGAACACTTTATCAGCCGGGAAATAATGCGGGCAACGGTGTTTAATTATATCGAATGTGATTACAATCGGTGGCGGCGGCACAGTTGGTGTGGCGGCCTCAGTCCGGAACAATTTGAAAACAAGAACCTCGCTTAGGCCTGTGGCCATATTACGTGGGTAGGATCAGTCATCCCTTCGTGGATCATTTTGACTGCCGCCGGCGCTATGCTGTTTTTTg                                                                                                                                                                                                        <  2:240422/249‑1 (MQ=255)                                                            gCTGAAAGTGGAATGTATCCATGGAGAACACTTGATCAGCCGGGAAATAATGCGGGCAACGGTGTTTAATTATATCGAATGTGATTACAATCGGTGGCGGCGGCACAGTTGGTGTGGCGGCCTCAGTCCGGAACAATTTGAAAACAAGAACCTCGCTTAGGCCTGTGTCCATATTACGTGGGTAGGATCAGTCATCCCTTCTTGGATCATTTTGACTGCCGCCTGCGCTATTCTGTTTTTTGGCGCGCTgg                                                                                                                                                                                               <  2:183085/251‑1 (MQ=255)                                                                               cATGGAGAACACTTTATCAGCCGGGAAATAATGCGGGCAACGGTGTTTAATTATATCGAATGTGATTACAATCGGTGGCGGCGGCACAGTTGGTGTGGCGGCCTCAGTCCGGAACAATTTGAAAACAAGAACCTCGCTTAGGCCTGTGTCCATATTACGTGGGTAGGATCAGTCATCCCTTCGTGGATCATTTTGACTGCCGCCTGCGCTATTCTGTTTTTTGGCGCGCTGGCGAGCTGAAATCGCTCttt                                                                                                                                                                            >  1:137044/1‑251 (MQ=255)                                                                                   gagaACACTTTATCAGCCGGGAAATAATGCGGGCAACGGTGTTTAATTATATCGAATGTGATTACAATCGGTGGCGGCGGCACAGTTGGTGTGGCGGCCTCAGTCCGGAACAATTTGAAAACAAGAACCTCGCTTAGGCCTGTGTCCATATTACGTGGGTAGGATCAGTCATCCCTTCGTGGATCATTTTGACTGCCGCCTGCGCTATTCTGTTTTTTGGCGCGCTGGCGAGCTGAAATCGCTCTTTAAAc                                                                                                                                                                        <  1:73498/251‑1 (MQ=255)                                                                                     gaACCCTTTATCAGTCGGGAAATAATGCGGGCAACGGTGTTTAATTATATCGAATGTGATTACAATCGGTGGCGGCGGCACAGTTGGTGTGGCGGACTCAGTCCGGAACAATTTGAAAACAAGAACCTCTCTTAGGCCTTTGTCCATATTACGTGGGTAGGATCAGTCATCCCTTCGTGGAGCATTTTGACTGCCGCCTGCGCTATTCTGTTTTTTGGCGCCCTGGCGAGCTGTAATCGCTCGTTAAAccc                                                                                                                                                                      <  2:348443/251‑1 (MQ=18)                                                                                        cacTTTATCAGCCGGGAAATAATGCGGGCAACGGTGTTTAATTATATCGAATGTGATTACAATCGGAGGCGGCGGCACAGTTGGTGTGGCGGCCTCAGTCCGGGACAATTTGAAAACAAGAACATCCCTTAGGCCTGTGACCATATTACGGGGGGAGGATCAGTCATCCCTTCGCGGATCATTTTATCTGCCGCCTGCGCTATTTTGGTTTTTAGCGCGCTGGCGGGCTGAAATCGCTCTTTAAACCCGAc                                                                                                                                                                   >  2:240609/1‑251 (MQ=18)                                                                                                                  ggCAACGGTGTGTAATTATATCGAAGGTGATTACAATCGGTGGCGGCGGCACAGTTGGTGTGGCGGCCTCAGTCCGGAACAATTTGAAAACAAGAACCGCGCTTAGGCCTGTGTCCATATTACGTGGGTAGGATCAGTCATCCCTTCGTGGATCATTTTGACTGCCGCCTGCGCTATGCTGTTTTTTGGCGCGCGGGCGAGCTGAAATCGCTCTTGAAACCCGTCTTCCTGGGTCTCGGGTTCACTATTAc                                                                                                                                         <  2:289894/251‑1 (MQ=21)                                                                                                                                                                 ggcACAGTGGGTGTGGCGGCCTCAGTCGGAAAAAATTTGAAAACAAGAACCCCGCTTAGGCCTGTGTCCATATTACGGGGGTAGGATCAGTCAGCCCTTCGTGGATCATTTTGACTGCCGCCTGCGCTATTCTGTTTTTTGGCGCGCGGGCGAGCTGAAATCGCTCTTTAAACCCGACTTCCGGGGTCTGGGTGTCACTATTACCAGCCTTTATTTTCGCCGCACCGCCATGAAAGCGCGTAACCACGCCt                                                                                          <  2:280725/251‑1 (MQ=255)                                                                                                                                                                    acaGTTGGTGTGGCGGCCTCAGTCCGGAACAATTTGCAAAAAAGCACCTCGCCAAGGCCTCAGCAAATATTAAGTGGGTAGCATCAGTCATCACTTCGTGGATCATTTTGACTGCCGCCTGCGCTATTCTGTTTTTTGGCACGCTGGAGAGCTGAAATCGCTCTTAAAACCCGACTTCCTGGGACTCGGTTTCACTATTACCAGACATTATTTTCGCCGCACCCCCATGAACGCGCGTAACCACGCCtttt                                                                                       >  1:25003/1‑251 (MQ=255)                                                                                                                                                                    acaGTTGGTGTGGCGGCCTCAGTCCGGAACAATTTGAAAACAAGACCCTCGCTTAGGCCTGTGTCCATATTACGTGGGTAGGATCAGTAATCCCTTCGTGGATCATTTTGACTGCCGCCTGCGCTATTCTGTTTTTTGGCGCGCTGGCGAGCTGAAATCGCTCTTTAAACCCGACTTCCTGGGTCTCGGTTTCACTATTACCAGACATTATTTTCGCCGCACCGCCATGAAAGCGCGTAACCACGCCtttt                                                                                       >  1:155712/1‑251 (MQ=255)                                                                                                                                                                                           ccGGAACAATTTGAAAACAAGAACCTCGCTTAGGCCTGTGTCCATATTCCGTGGGTAGGATCAGTCATCCCTTCGTGGATCATTTTGACTGCCGCCTGCGCTATTCTGTTTTTTGGCGCGCTGGCGAGCTGAAATCGCTCTTTAAACCCGACTTCCTGGGTCTCGGTTTCACTATTACCAGACATTATTTTCGCCGCACCGCCATGAAAGCGCGTAACCACGCCTTTTTGTTCGAGAAAGCGCAAATCGGc                                                                <  1:93099/251‑1 (MQ=255)                                                                                                                                                                                                     ttGAAAACAAGAACCTCGCTTAGGCCTGTGTCCATTTTACGTGGGTAGGATCAGTCATCCCTTCGTGGATCATTTTGACTGCCGCCTGCGCTATTCTGTTTTTTGGCGCGCTGGCGAGCTGAAATCGCTCTTTAAACCCGACTTCCTGGGTCTCGGTTTCACTATTACCAGACATTATTTTCGCCGCACCGCCATGAAAGCGCGTAACCACGCCTTTTTGTTCGAGAAAGCGCAAATCGGCACGGATTGt                                                       <  1:14149/250‑1 (MQ=255)                                                                                                                                                                                                         aaaCAAGCACCCCGGTTAGGCCTGTGTCCATATTACGGGGGTAGGATCAGTCATCCCTTCGTGGATCATTTTGGCTGCCGCCTGCGCTATTCTGTTTTTTGGCGCGCGGGCGAGCGGAAATCGCTCTTAAAACCCGACTTCCTGGTTCGCGGTTTCACTATTACAAGACATTATTTTCGCCGCACCGCCATGAAAGCGCGTAACCACGCCTTTTTGTTCGAGAAAGCGCAAATCGGCACGGATTGTCGCtt                                                  <  2:95374/251‑1 (MQ=255)                                                                                                                                                                                                                 aCCTCACTTAGGCCTGTGTCCATATTAAGCGGGTAGGATCAGTCATCCCTTCGTGGATCATTTTGACTGCCGCCTGCGCTATTCTGTTTTTTGGCGCGCTGGCGAGCTGAAATCGCTCTTTAAACCCGACTTCCTGGGTCTCGGTTTCACTATTACCAGACATTATTTTCGCCGCACCGCCATGAAAGCGCGTAACCACGCCTTTTTGTTCGAGAAAGCGCAAATCGGCACGGATTGTCGCTTCCGAGgc                                           >  2:22570/1‑250 (MQ=255)                                                                                                                                                                                                                                gtgtCCATATTACGTGGGTAGGATCAGTCATCCCTTCGTGGATCATTTTGACTGCCGCCTGCGCTATTCTGTTTTTTGGCGCGCTGGCGAGCTGAAATCGCTCTTTAAACCCGACTTCCTGGGTCTCGGTTTCACTATTACCAGACATTATTTTCGCCGCACCGCCATGAAAGCGCGTAACCACGCCTTTTTGTTCGAGAAAGCGCAAATCGGCACGGATTGTCGCTTCCGAGGCAGCAAATACTCCCGcc                           >  1:263731/1‑251 (MQ=255)                                                                                                                                                                                                                                                    ggATCAGTCATCCCTTCGTGGATCATTTTGACTGCCGCCTGCGCTATTCTGTTTTTTGGCGCGCTGGCGAGCTGAAATCGCTCTTTACACCCGACTTCCTGGGTCTCGGTTTCACTATTACCAGACATTATTTTCGCCGCACCGCCATGAAAGCGCGTAACCACGCCTTTTTGTTCGAGAAAGCGCAAATCGGCACGGATTGTCGCTTCCGAGGCAGCAAATACTCCCGCCAGATCCTGAACAAGCACGGt       >  2:340239/1‑251 (MQ=255)                                                                                                                                                                                                                                                         aGTCATCCCTTCGTGGATCATTTTGACTGCCGCCTGCGCTATTCTGTTTTTTGGCGCGCTGGCGAGCTGAAATCGCTCTTTAAACCCGACTTCCTGGGTCTCGGTTTCACTATTACCAGACATTATTTTCGCCGCACCGCCATGAAAGCGCGTAACCACGCCTTTTTGTTCGAGAAAGCGCAAATCGGCACGGATTGTCGCTTCCGAGGCAGCAACTACTCCCGCCAGATCCTGACCAAGCACGGTTCCCt  >  1:278104/1‑251 (MQ=255)                                                                                                                                                                                                                                                         |                                                                                                                                                                                                                                                           AGTATGAGCGCAAAAGGTTGCTGCTACGATAATGCCTGCGTGGAAAGCTTCTTTCATTCGCTGAAAGTGGAATGTATCCATGGAGAACACTTTATCAGCCGGGAAATAATGCGGGCAACGGTGTTTAATTATATCGAATGTGATTACAATCGGTGGCGGCGGCACAGTTGGTGTGGCGGCCTCAGTCCGGAACAATTTGAAAACAAGAACCTCGCTTAGGCCTGTGTCCATATTACGTGGGTAGGATCAGTCATCCCTTCGTGGATCATTTTGACTGCCGCCTGCGCTATTCTGTTTTTTGGCGCGCTGGCGAGCTGAAATCGCTCTTTAAACCCGACTTCCTGGGTCTCGGTTTCACTATTACCAGACATTATTTTCGCCGCACCGCCATGAAAGCGCGTAACCACGCCTTTTTGTTCGAGAAAGCGCAAATCGGCACGGATTGTCGCTTCCGAGGCAGCAAATACTCCCGCCAGATCCTGAACAAGCACGGTTCCCT  >  NC_000913/2171180‑2171678

Alignment Legend
Aligned base mismatch/match (shaded by quality score): ATCG/ATCG < 3 ≤ ATCG/ATCG < 13 ≤ ATCG/ATCG < 14 ≤ ATCG/ATCG < 31 ≤ ATCG/ATCG < 39 ≤ 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.