Predicted mutation
evidence	seq id	position	mutation	annotation	gene	description
JC JC	NC_000913	3,720,136	IS3 (–) +3 bp :: +TCA	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	315229 =	NA (NA)	27 (0.900) +TCA	26/480	0.2	96.4%	noncoding (1/1255 nt)	IS3	repeat region
	?	NC_000913	3720136 =	1 (0.030)					coding (88/213 nt)	cspA	cold shock protein CspA
*	?	NC_000913	= 2171428	NA (NA)	38 (1.250)	35/484	0.1	100%	noncoding (1258/1258 nt)	IS3	repeat region
	?	NC_000913	= 3720138	0 (0.000)					coding (90/213 nt)	cspA	cold shock protein CspA

ATGAGCGCAAAAGGTTGCTGCTACGATAATGCCTGCGTGGAAAGCTTCTTTCATTCGCTGAAAGTGGAATGTATCCATGGAGAACACTTTATCAGCCGGGAAATAATGCGGGCAACGGTGTTTAATTATATCGAATGTGATTACAATCGGTGGCGGCGGCACAGTTGGTGTGGCGGCCTCAGTCCGGAACAATTTGAAAACAAGAACCTCGCTTAGGCCTGTGTCCATATTACGTGGGTAGGATCAGTCATCCCTTCGTGGATCATTTTGACTGCCGCCTGCGCTATTCTGTTTTTTGGCGCGCTGGCGAGCTGAAATCGCTCTTTAAACCCGACTTCCTGGGTCTCGGTTTCACTATTACCAGACATTATTTTCGCCGCACCGCCATGAAAGCGCGTAACCACGCCTTTTTGTTCGAGAAAGCGCAAATCGGCACGGATTGTCGCTTCCGAGGCAGCAAATACTCCCGCCAGATCCTGAACAAGCAC  >  NC_000913/2171183‑2171670                                                                                                                                                                                                                                                      |                                                                                                                                                                                                                                                   aTGAGCGCAACAGGCTGCTGCTACGATAATGACTGCGTGGAAAGCTTCTTTCATTCGCTGCACGTGGCATGTCTCCATGGAGAACACTTTATCAGCCGGGAAATAATGCGGGCAACGGTGTTTAATTATATCGAATGTGATTACAATCGGTGGCGGCGGCCCAGTTGGTGTGGCGGCCTCAGTCCGGAACAATTTGAAAACAAGAACCTCGCTTAGGCCTGTGTCCATATTACGTGGGTAGGAACAGTCAt                                                                                                                                                                                                                                               >  2:114602/1‑251 (MQ=11)    aGCGCAAAAGGTTGCTGCTACGATAATGCCTGCGTGGAAAGCTTCTTTCATTCGCTGAAAGTGGAATGTATCCATGGAGAACACTTTATCAGCCGGGAAATAATGCGGGCAACGGTGTTTAATTATATCGAATGTGATTACAATCGGTGGCGGCGGCACAGTTGGTGTGGCGGCCTCAGTCCGGAACAATTTGAAAACAAGAACCTCGCTTAGGCCTGTGTCCATATTACGTGGGTAGGATCAGTCATccc                                                                                                                                                                                                                                            <  2:246070/251‑1 (MQ=33)         aaaaGGTTGCTGCTACGATAATGCCTGCGTGGAAAGCTTCTTTCATTCGCTGAAAGTGGAATGTATCCATGGAGAACACTTTATCAGCCGGGAAATAATGCGGGCAACGGTGTTTAATTATATCGAATGTGATTACAATCGGTGGCGGCGGCACAGTTGGTGTGGCGGCCTCAGTCCGGAACAATTTGAAAACAAGAACCGCGCTTAGGCCTGTGTCCATATTACGTGGGTAGGATCAGTCATCCCTTCGt                                                                                                                                                                                                                                       <  1:33448/251‑1 (MQ=25)                       aCGATAATGCCTGCGTGGAAAGCTTCTGTCATTCGCTGAAAGTGGAATGTATCCATGGAGAACACTTTATCAGCCGGGAAAGAATGCGGGCAACGGTGTTTAATTATATCGAATGTGATTACAATCGGTGGCGGCGGCACAGTTGGTGTGGCGGCCTCAGTCCGGAACAATTTGAAAACAAGAACCTCGCTTAGGCCTGTGTCTATATTACGTGGGTAGGATCAGTCATCCCTTCGTGGATCATTTTGACt                                                                                                                                                                                                                         <  1:296941/251‑1 (MQ=255)                            aaTGCCTGCGTGAAAAGCTTCTTTCATTCGCTGAAAGTGGAATGTATCCATGGAGCACACTTTATCAGCCGGGAAATAATGCGGGCGACGGTGTTTAATTATATCGATTGTGATTACATTCGGTGGCGGCGGCACAGTTGGTGTGGCGGCCTCAGTCCGGAACAATTTGACAACCAGAACCTTGATTAGGGCTGTGGCCATATTACGAGGGGAGGATCAGTCATCCCTTCGTGGATCATTTTGACTgccgc                                                                                                                                                                                                                    >  2:256531/1‑251 (MQ=14)                                               tcttTCATTCGCTGAAAGTGGAATGTATCCATGGAGAACACTTTATCAGCCGGGAAATAATGCGGGCAACGGTGTTTAATTATATCGAATGTGATTACAATCGGTGGCGGCGGCACAGTTGGTGTGGCGGCCTCAGTCCGGAACAATTTGAAAACAAGAACCGCGCTTAGGCCTGTGTCCATATTACGTGGGTAGGATCAGTCATCCCTTCGTGGATCATTTTGACTGCCGCCGGCGCTATTCTGttttt                                                                                                                                                                                                  <  1:264171/250‑1 (MQ=255)                                               tcgttCATTCGCTGAAAGTTGAATGTATCCATGGAGAACACTTTATCAGCCGGGAAATAATGCGGGCAACGGTGTTTAATTATATCGAATGTGAGTACAATCGGTGGCGGCGGCACAGTTGGTGTTGCGGCCTCAGTCCGGAACAATTTTAAAACAAGAACCGCGCTTAGGCCGGTGTCCATATTACGTGGGTAGGATCATTCATCCCGTCGGGGAGCATTTTGACTGCCGCCTGCGCTAGTCTGgttt                                                                                                                                                                                                   <  2:261748/246‑1 (MQ=14)                                                            gAAAGTGGAATGTATCCATGGAGAACACTTTATCAGCCGGGAAATAATGCGGGCAACGGTGTTTAATTATATCGAATGTGATTACAATCGGTGGCGGCGGCACAGTTGGTGTGGCGGCCTCAGTCCGGAACAATTTGAAAACAAGAACCTCGCTTAGGCCTGTGTCCATATTACGTGGGTAGGATCAGTCATCCCTTCGTGGATCATTTTGACTGCCGCCTGCGCTATTCTGTTTTTTGGCGCGCTGGc                                                                                                                                                                                      <  1:261601/249‑1 (MQ=255)                                                                            cagggAGACCACTTTATCAGCCGGGAAATAATGCGGGCAGCGGTGTTTAAGTATATCGAATGTGATTACAATCGGTGGCGGCGGCACAGTTGGTGTGGCGGCCTCAGTCCGGAACAATTTGAAAACAAGAACCTCGCTTAGGCCTGTGTCCCTATTACGTGGGTAGGATCAGTCATCCCTTCGTGGATCATTTTGACTGCCGCCTTCTCTATTCTGAATTGTGGCGCACTGGCGAGCTGGAATGGCTCttt                                                                                                                                                                    <  2:201267/248‑1 (MQ=17)                                                                                          tATCAGCCGGGAAATAATGCGGGCAACGGTGTTTAATTATATCGAATGTGATGACAATCGGTGGCGGCGGCACAGTTGGTGTGGCGGACTCAGTCCGGAACAATTTGAAAACAAGAACCTCGCGTAGTCCTTTGTCCATATTACGTGGGTATGAGCAGTCATCCCTTCGTGGATCATTTTGACTGCCGCCTGCGCTATTCTGTGTTTTGGCGCGCTGGCGAGCTGAAATCGCTCTTTAAACCCGACTTcc                                                                                                                                                       <  1:131211/250‑1 (MQ=21)                                                                                                 cGGGAAATAATGCGGGCAACGGTGTTTAATTATATCGAATGTGATTACAATCGGTGGCGGCGGCACAGTTGGTGTGGCGGCCTCAGTCCGGAACAATTTGAAAACAAGAACCTCGCTTAGGCCTGTGTTCATATTACGTGGGTAGGATCAGTCATCCCTTCGTGGATCATTTTGACTGCCGCCTGCGCTATTCTGTTTTTTGGCGCGCTGGCTAGCTGAAATCGCTCTTTAAACCCGACTGCCTTGGtctc                                                                                                                                               <  2:271560/251‑1 (MQ=255)                                                                                                   ggAAATAATGCGGGCAACGGTGTTTAATTATATCGAATGTGATTACAATCGGTGGCGGCGGCACAGTTGGTGTGGCGGCCTCAGTACGGAACAATTTGAAAACAAGAACCTCGCTTAGGCCTGTGTCCATATTACGTGGGTAGGATCAGTCATCCCTTCGTGGATCATTTTGACTGCCGCCTGCGCTATTCTGTTTTTTGGCGCGCTGGCGAGCTGAAATCGCTCTTTAAACCCGCATTCCTGGGTCTCgg                                                                                                                                             >  2:54552/1‑251 (MQ=255)                                                                                                    gAAATAATGCGGGCAACGGTGTTTAATTATATCGAATGTGATTACAATCGGTGGCGGCGGCACAGTTGGTGTGGCGGCCTCAGTCCGGAACAATTTGAAAACAAGAACCTCGCTTAGGCCTGTGTCCATATTACGTGGGTAGGATCAGTCATCCCTTCGTGGATCATTTTGACTGCCGCCTGCGCTATTCTGTTTTTTGGCGCGCTGGCGAGCTGAAATCGCTCTTTAAACCCGACTTCCTGGGTCTCGGt                                                                                                                                            <  1:256349/251‑1 (MQ=255)                                                                                                                             aTTATAGCGAATGTGATTACAATCGGTGGCGGCGGCACAGTTGGTGTGGCGGCCTCAGTCCGGAACAATTTGAAAACAAGAACCTCGCTTAGGCCTGTGTCCATATTACGTGGGTAGGATCAGTCATCCCTTCGTGGATCATTTTGACTGCCGCCTGCGCGATTCTGTTTTGTGGCGCGCTGGCGAGCTGAAATCGCTCTTTAAACCCTACTTCCTGGGTCTCGGTTTCACTATTACCAGACATTATTTTc                                                                                                                   <  1:41448/251‑1 (MQ=255)                                                                                                                                        ggtgATTACAATCGGTGGCGGCGGCACAGTTGGTGTGGCGGCCTCAGTCCGGAACAATTTGAAAACAAGAACCTCGCTTAGGCCTGTGTCCATATTACGTGGGTAGGATCAGTCATCCCTTCGTGGATCATTTTGACTGCCGCCTTCGCTATTCTGTTTTTTGGCGCGCTGGCGAGCTGAAATCGCTCTTTAAACCCGACTTCCTGGGTCTCGGTTTCACTATTACCAGACATTATTTTCGCCGCACCGcc                                                                                                        <  2:236302/250‑1 (MQ=255)                                                                                                                                           gATTACAATCGGTGGCGGCGGCACAGTGGGTGTGGCGGCCTCAGTCCGGAACAATTTGAAAACAAGAACCTCGCTTAGGCCTGTGTCCATATTACGTGGGTAGGATCAGTCATCCCTTCGTGGATCATTTGGACTGCCGCCTGCGCTATTCTGTTTTTTGGCGCGCGGGCGAGCTGAAGTCGCTCTTTAAACCCGACTTCCTGGGTCTCGGTTTCACTATTATCAGACATTATTTTCGCCGCACCGCCATg                                                                                                     <  1:114602/251‑1 (MQ=255)                                                                                                                                                     ggTGGCGGCGGCACAGTTGGTGTGGCGGCCTCAGTCCGGAACAATTTGCAAACAAGAACCTCGCTTAGGCCTGTGTCCATATTACGTGGGTAGGATCAGTCATCCCTTCGTGGATCATTTTGACTGCCGCCTGCGCTATTCTGTTTTTTGGCGCGCTGGCGAGCTGAAATCGCTCTTTAAACCCGACTTCCTGGGTCTCGGTTTCACTATTACCAGACATTATTTTCGCCGCACCGCCATGAAAGCGCGt                                                                                            >  1:16460/1‑250 (MQ=255)                                                                                                                                                                                      gTCCGGAACAATTTGAAAACAAGAACCTCGCTTAGGCCTGTGTCAATATTACGTGGGTAGGAGCAGTCATCCCTTCGTGGATCATTTGGACGGCCGCCTGCGCTATTCTGTTTTTTGGCGCGCTGGCGAGCTGAAATCGCTCTTTAAACCCGACTCCCTGGGTCTCGGTTTCACTATTACCAGACATTATTTTCGCCGCACCGCCATGAAAGCGCGTAACCACGCCTTTTTGTTCGAGAAAGCGCAAATCg                                                          <  1:197311/251‑1 (MQ=255)                                                                                                                                                                                           gAACAATTTGAAAACAAGACCCTCGCTTAGGCCTGGGTCCATTTTACGTGGGTAGGATCAGTCATCCCTCCGTGGATGATTTTGACTTCCGCCTGCGTTATTCTGTTTTTGGGCGCGCGGGCGAGCTGAAATCTCTCTTTAAACCCGACTTCCGGGGTCTCGGTTTCACTATTACCACTCATTATTTTCGCCGCACCGCCATGAAAGCGCGTAACCACGCCTTTTTGTTCGAGAAAGCGCAAATCGGCACg                                                     <  1:293979/251‑1 (MQ=255)                                                                                                                                                                                              cAATTTGAAAACAAGAACCCCGCTTAGGCCTGTGTCCATATTACGTGGGTAGGATCAGTCATCCCTTCGTGGATCATTTTGACTGCCGCCTGCGCTATTCTGTTTTTTGGCGCGCTGGCGAGCTGAAATCGCTCTTTAAACCCGACTTCCTGGGTCTCGGTTTCACTATTCCCAGACATTATTTTCGCCGCACCGCCATGAAAGCGCGTAACCACGCCTTTTTGTTCGAGAAAGCGCAAATCGGCACGGAt                                                  <  2:112203/251‑1 (MQ=255)                                                                                                                                                                                                aTTTGAAAACAAGAACCTCGCTTAGGCCTGTGTCCATATTACGTGGGTAGGATCAGTCATCCCTTCGTGGATCATTTTGACTGCCGCCTGCGCTATTCTGTTTTTTGGCGCGCTGGCGAGCTGAAATCGCTCTTTAAACCCGACTTCCTGGGTCTCGGTTTCACTATTACCAGACATTATTTTCGCCGCACCGCCATGAAAGCGCGTAACCACGCCTTTTTGTTCGAGAAAGCGCAAATCGGCACGGATTg                                                >  1:241572/1‑251 (MQ=255)                                                                                                                                                                                                                               gtCCATATTACGTGGGTAGGATCAGTCATCCCTTCGTGGATCATTTTGCCTGCCGCCTGCGCTATTCTGTTTTTTGGCGCGCTGGCGAGCTGAAATCGCTCTTTAAACCCGACTTCCTGGGTCTCGGTTTCACTATTACCAGACATTATTTTCGCCGCACCGCCATGAAAGCGCGTAACCACGCCTTTTTGTTCGAGAAAGCGCAAATCGGCACGGATTGTCGCTTCCGAGGCAGCAAATCCTCCCGcc                   >  1:290850/1‑249 (MQ=255)                                                                                                                                                                                                                                          gTGGGTAGGCTCAGTCATCCCTTCGTGGATCATTTTGACTGCCGCCTGCGCTATTCTGTTTTTTGGCGCGCTGGCGAGCTGAAATCGCTCTTTAAACCCGACTTCCTGGGTCTCGGTTTCACTATTACCAGACATTATTTTCGCCGCACCGCCATGAAAGCGCGTAACCACGCCTTTTTGTTCGAGAAAGCGCAAATCGGCACGGATTGTCGCTTCCGAGGCAGCAAATACTCCCGCCAGATCCTGAACa       >  1:240985/1‑250 (MQ=255)                                                                                                                                                                                                                                              gTAGGATCAGTCATCCCTTCGTGGATCATTTTGACTGCCGCCTGCGCTATTCTGTTTTTTGGCGCGCTGGCGAGCTGAAATCGCTCTTTAAACCCGACTTCCTGGGTCTCGGTTTCACTATTACCAGACATTATTTTCGCCGCACCGCCATGAAAGCGCGTAACCACGCCTTTTTGTTCGAGAAAGCGCAAATCGGCACGGATTGTCGCTTCCGAGGCAGCAAATACTCCCGCCAGATCCTGAACAAGCAc  >  1:171321/1‑251 (MQ=255)                                                                                                                                                                                                                                                      |                                                                                                                                                                                                                                                   ATGAGCGCAAAAGGTTGCTGCTACGATAATGCCTGCGTGGAAAGCTTCTTTCATTCGCTGAAAGTGGAATGTATCCATGGAGAACACTTTATCAGCCGGGAAATAATGCGGGCAACGGTGTTTAATTATATCGAATGTGATTACAATCGGTGGCGGCGGCACAGTTGGTGTGGCGGCCTCAGTCCGGAACAATTTGAAAACAAGAACCTCGCTTAGGCCTGTGTCCATATTACGTGGGTAGGATCAGTCATCCCTTCGTGGATCATTTTGACTGCCGCCTGCGCTATTCTGTTTTTTGGCGCGCTGGCGAGCTGAAATCGCTCTTTAAACCCGACTTCCTGGGTCTCGGTTTCACTATTACCAGACATTATTTTCGCCGCACCGCCATGAAAGCGCGTAACCACGCCTTTTTGTTCGAGAAAGCGCAAATCGGCACGGATTGTCGCTTCCGAGGCAGCAAATACTCCCGCCAGATCCTGAACAAGCAC  >  NC_000913/2171183‑2171670

Alignment Legend
Aligned base mismatch/match (shaded by quality score): ATCG/ATCG < 3 ≤ ATCG/ATCG < 13 ≤ ATCG/ATCG < 14 ≤ ATCG/ATCG < 32 ≤ 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.