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 (0.890) +TCA	25/484	0.3	100%	noncoding (1/1255 nt)	IS3	repeat region
	?	NC_000913	3720136 =	0 (0.000)					coding (88/213 nt)	cspA	cold shock protein CspA
*	?	NC_000913	= 2171428	NA (NA)	25 (0.810)	25/488	0.3	100%	noncoding (1258/1258 nt)	IS3	repeat region
	?	NC_000913	= 3720138	0 (0.000)					coding (90/213 nt)	cspA	cold shock protein CspA

AGGTTGCTGCTACGATAATGCCTGCGTGGAAAGCTTCTTTCATTCGCTGAAAGTGGAATGTATCCATGGAGAACACTTTATCAGCCGGGAAATAATGCGGGCAACGGTGTTTAATTATATCGAATGTGATTACAATCGGTGGCGGCGGCACAGTTGGTGTGGCGGCCTCAGTCCGGAACAATTTGAAAACAAGAACCTCGCTTAGGCCTGTGTCCATATTACGTGGGTAGGATCAGTCATCCCT‑TCGTGGATCATTTTGACTG‑CCGCCTGCGCTATTCTGTTTTTTGGCGCGCTGGCGAGCTGAAATCGCTCTTTAAACCCGACTTCCTGGGTCTCGGTT‑TCACTATTACCAGACATTATTTTCGCCGCACCGCCATGAAAGCGCGTAACCACGCCTTTTTGTTCGAGAAAGCGCAAATCGGCACGGATTGTCGCTTCCGAGGCAGCAAATACTCCCGCCAGATCCTGAACAAGCACGGTTC  >  NC_000913/2171194‑2171675                                                                                                                                                                                                                                           |                                                                                                                                                                                                                                                           aGGTTGCTGCTACGATAATGCCTGCGTGGCAAGCTTCTTTCATTCGCTGCCAGCGGAATGTCTCCATGGACAACACTTTAACCGCCGGGACATAATGCGGGCAACGGTGTTTAATTATCTCGAATGTGCTTACAATCGGTGGCGGCGGCACAGTTGGTGTGGCGGCCTCAGTCCGGAACAATTTGAAAACCAGAACCTCGCTTAGGCCTGTGTCCATATTACGTGGGTAGGATCCGTCATCCCT‑TCGTgg                                                                                                                                                                                                                                            >  1:285313/1‑250 (MQ=11)           tACGATAAAGCCTGCGTGAAAAGCTTCTTTCATTCGCTGAAAGTGGAATGTATCCATGGAGAACACTTTATCCGCCGGGAAATAATGCGGGCAACGGTGTTTAATTATATCGAATGTGATTACAATCGGTGGCGGCGGCACAGTTGGTGTGGCGGCCTCAGTCCGGAACACTTTGAAAACCAGAACCTCGCTTAGGCCTGTGTCCATATTTCGTGGGTATGCTCAGTCATCCCT‑TCGTGGATCCtttttac                                                                                                                                                                                                                                 >  2:281167/1‑248 (MQ=11)                                 gCTTCTTTCATTCGCTGAAAGTGGAATGTATCCATGGAGAACACTTTATCAGCCGGGAAATAATGCGGGCAACGGTGTTTAATTATATCGAATGTGATTACAATCGGTGGCGGCGGCACAGTTGGTGTGGCGGCCTCCGTCCGGAACAATTTGAAAACAAGGACCCCGATTAGGCCTGTGTCCATATTACGTGGGTAGGATCAGGCATCCCT‑TCTTGGATAATTTTGACTG‑CCGCCTGCTCTATTCTGttt                                                                                                                                                                                                          >  2:161735/1‑251 (MQ=14)                                    tctgtCATTCGCTGAAAGTGGAAGGTAACCATGGAGAACACCGTATCAGCCGGGAAATAATGCGGGCAACGGTGTTTAATTATATCGAATGTGATTACAATCGGTGGCGGCGGCACAGTTGGTGTGGCGGCCTCAGTCCGGAACAATTTGAAAACAAGAACCTCGCTTAGGCCTGTGTCCATATTACGTGGGTAGGATCAGTCATCCCT‑TCGTGGATCATTTTGACTG‑CCGCCTTCGCTATGCTGttttt                                                                                                                                                                                                        <  2:255930/246‑1 (MQ=17)                                               gtGAAAGTGGAATGTATCCATGGAGAACACTTTATCAGCCGGGAAATAATGCGGGCAACGGTGTTTAATTATATCGAATGTGATTACAATCGGTGGCGGCGGCACAGTTGGTGTGGCGGCCTCAGTCCGGAACAATTTGAAAACAAGAACCGCGCTTAGGCCTGTGTCCATATTACGTGGGTAGGATCAGTCATCCCT‑TCGTGGATCATTTTGACTG‑CCGCCTGCGCTATTCTGTTTTTTGGCGCGCTGGc                                                                                                                                                                                            <  2:228684/250‑1 (MQ=255)                                                 gAAAGTGGAATGTATCCATGGAGAACACTTTATCAGCCGGGAGATACAGCGGGCAAAGGTGTTTAATTATATCGCCTGTGATTACAATCGGAGGCGGCGGCACAGTTTGTGTGGCGGCCTCAGTCCGGAACAATTTGAAAACAAGAACCTCGCTTAGGCCTGTGTCCATATTACGTGGGTAGGAATAGTCATCCCT‑TCGTGGATCATTTTTTCTG‑CCGGCTTCGCTCTTCTGTTTTTTTgcgctcgtgcgg                                                                                                                                                                                          >  2:43248/1‑243 (MQ=14)                                                     gTGGAATGTATCCATGGAGAACACTTTATCAGCCGGGACCTAGTGCGGGCACCGGTGTTTCATTCTATAGAATGAGCTCCCAATAGACGGCGGCGCCACCGTTACTGCGGCGCCCTCACTCCGGAACCATTTGAAAACAAGAAAATACCTTAGGACTGCCACCCTATTCCGTGGGTAGGATCAGTCATCCAT‑TCGTGGCTCATTTTGCCTG‑CCGCCCGCGCTCTACTGTTTTTTGGCGCGCTGGCGAGCTg                                                                                                                                                                                      >  1:192210/1‑251 (MQ=255)                                                         aaTGTATCCATGGAGAACACTTTATCAGCCGGGAAATAATGCGGGCACCGGTGTTTAATTATATCGAATGTGATTACAATCGGTGGCGGCGGCACAGTTGGTGTGGCGGCCTCAGTCCGGAACAATTTGAAAACAAGAACCTCGCTTAGGCCTGTGTCCATATTACGTGGGTAGGATCAGTCATCCCC‑TCGTGGATCATTTTGACTG‑CCGCCTGCGCTATTCTGTTTTTTGGCGCGCTGGCGAGCTGAAAt                                                                                                                                                                                  >  1:179826/1‑251 (MQ=255)                                                                ccATGGAGAACACTTTATCAGCCGGGAAATAATGCGGGCAACGGTGTTTAATTATATCGAATGTGATTACAATCGGTGGCGGCGGCACAGTTGGTGTGGCGGCCTCAGTCCGGAACAATTTGAAAACAAGAACCTCGCTTAGGCCTGTGTCCATATTACGTGGGTAGGATCAGTCATCCCT‑TCGTGGATCATTTTGACTG‑CCGCCTGCGCTATTCTGTTTTTTGGCGCGCTGGCGAGCTGAAATCGctct                                                                                                                                                                            <  2:70796/250‑1 (MQ=255)                                                                                     ccGGGAAATAATGCGGGCAACGGTGTTTAATTATATCGAATGTGATTAAACTCGGTGGCGGCGGCACAGTTGGTGTGGCGGCCTCAGTCCGGAACAATTTGCAAACAAGAAACTCGCTTAGGCCTGTGTCCATATTACGTGGGTAGGATCAGTCATCCCT‑TCGCGGATCATTTTGACTG‑CCGCCTGCGCTATTCTGTTTTTTGGCGCGCTGGCGAGCTGAAATCGCTCTTTAAACCCGACTTCCTGGGtcc                                                                                                                                                      >  1:173960/1‑250 (MQ=255)                                                                                       gggAAAGAATGCTGGCAACGGTGTTTAATTATATCGAATGTGATTACAATCGGTGGCGGCGGCACAGTTGGTGTGGCGGCCTCAGTCCGGAACAATTTGAAAACAAGAACCTCGCTTAGGCCTGTGTCCATATTACGTGGGTAGGATCAGTCATCCCT‑TCGTGGATCATTTTGACTG‑CCGCCTGCGCTATTCTGTTTTTTGGCGCGCTGGCGAGCTGAAATCGCTCTTTAAACCCGACTTCCCGGGTCTCg                                                                                                                                                    <  2:244724/251‑1 (MQ=255)                                                                                         gAAATAATGCGGGCAACGGTGTTTAATTATATCGAATGTGATTACAATCGGTGGCGGCGGCACAGTTGGTGTGGCGGCCTCAGTCCGGAACAATTTGAAAACAAGAACCTCGCTTAGGCCTGTGTCCATATTACGTGGGTAGGATCAGTCATCCCT‑TCGTGGATCATTTTGACTG‑CCGCCTGCGCTATTCTGTTTTTTGGCGCGCTGGCGAGCTGAAATCGCTCTTTAAACCCGACTTCCTGGGTCTCGGt                                                                                                                                                  <  1:40262/251‑1 (MQ=255)                                                                                                 gcgtgCAACGGTGTTTAATTATATCGAATGTGATTACAATCGGTGGCGGCGGCACAGTTGGTGTGGCGGCCTCAGTCCGGAACAATTTGAAAACAAGAACCGCGCTTAGGCCTGTGTCCATATTACGTGGGTAGGATCAGTCATCCCT‑TCGTGGATCATTTTGACTT‑CCGCCTGCGCTATTCGGTGTTTTGGCGCGCTGGGGAGCTGAAATCGCTCTTTAAACCCGACTTCCTGGGTCTCGGTT‑TCACTa                                                                                                                                          <  1:26048/246‑1 (MQ=255)                                                                                                  cGGGCAACGGTGTTTAATTATATCGAATGTGATTACAATCGGTGGCGGGGGCACAGTTGGTGTGGCGGCCTCAGTCCGGAACAATTTGAAAACAAGAACCTCGCTTAGGCCTGTGTCCATATTACGTGGGTAGGATCAGTCATCCCT‑TCGTGGATCATTTTGACTG‑CCGCCTGCGCTATTCTGTTTTTTGGCGCGCTGGCGAGCTGAAATCGCTCTTTAAACCCGACTTCCTGGGTCTCGGTT‑TCACTAtt                                                                                                                                        <  2:165583/251‑1 (MQ=255)                                                                                                    ggCAACGGTGTTTAATTATATCGAATGGGATTACAATCTGTGGCGGCGGCACAGTTGGTGTGGCGGCCTCAGTCCGGAACAATTTGAAAACAAGAACCTCGCTTAGGCCTGTGTCCATATGACGTGGGTAGGATCAGTCATCCCT‑TCGTGGATCATTTTGACTG‑CCGCCTGCGCTATTCTGTGTTTTGGCGCGCTGGCTAGCTGAAATCGCTCTTTAAACCCGACTTCCTGGGTCTCGGTT‑TCACTATTAc                                                                                                                                      <  1:142581/251‑1 (MQ=255)                                                                                                                     gtatCGAATGTGATTACAATCGGTGGCGGCAGCACAGTTGGTGGGGCGGCCTCAGTCCGGAACAATTTGAAAACAAGAACCTCGCTTCGGCCTGTGTCCATGTTACGTGGGTAGGATCATTCATCCCT‑TCGTGGATCATTTTGACTG‑CCGCCTGCGCTATTCTGTTTTTTGGCGCGCTGGGGATCTGCAATCGCTCTTTAAACCCGACTTCCTGTGTCTCGGTT‑TCACTATTACCAGACATTATTTTcgcc                                                                                                                     <  2:89170/250‑1 (MQ=25)                                                                                                                                gcttACAATCGGTGGCGGCGGCACAGTTGGTGTGGCGGCATCAATACCGAAAACTTTGAAAACAAGACCCTCGCGTAAGCCTGTGTCCAAATTACGTGGGTAGGATCAGACATCCCT‑TCGAGGAACATTTTGACTG‑CCGCCTGCGCTATTCTGTTTTTTGGCGAGCTGGCGAGCTGAAATCGCTCTTTAAAACCGCCTTCCTGGGTCTCGGTT‑TCACTATTACCAGACCTTATTTTCGCCGTACAGCCATg                                                                                                          >  2:21316/3‑251 (MQ=25)                                                                                                                                          ggTGGCGGCGGCACAGTTGGTGTGGCGGCCTCAGTCCGGGACACTTTGAAAACAAGAACCTCGCTTAGGCCTGTGTCCATATTACGTGGGTAGGATCAGTCATCCCT‑TCGTGGATCATTTTGACTG‑CCGCCTGCGCTATTCTGTTTTTTGGCGCGCTGGCGAGCTGAAATCGCTCTTTAAAACCGACTTCCTTGGTCTCGGTT‑TCACTATTACCAGACATTATTTTCGCCGCACCGCCATGAAAGCGCGt                                                                                                 >  1:106788/1‑250 (MQ=255)                                                                                                                                                   ggcccaGTTGGTGTGGCGGCCTCAGTCCGGAACAATTTGAAAACAAGAACCTCGCTTAGGCCTGTGTCCATATTACGTGGGTAGGATCAGTCATCCCT‑TCGTGGATCATTTTGACTG‑CCGCCTGCGCTATTCTGTTTTTTGGCGCGCTGGCGAGCTGAAATCGCTCTTTAAACCCGACTTCCTGGGTCTCGGTT‑TCACTATTACCAGACATTATTTTCGCCGCGCCGCCATGAAAGCGCGTAACCACGCCt                                                                                       <  1:232559/247‑1 (MQ=255)                                                                                                                                                       caGTGGGTGTGGCGGCCGCAGTCCGGAACAATTTAAAAACAAGATCCCCGCTTAGGCCTGTGTCCATATTCCGTGGGGAGGATCGGTCATCCCT‑TCGTGGATCATTTTGCCTG‑CCGCCTGTGCTATTCTGTTTTTTGGCGCGCTGGCGAGCTGAAATCGCTCTTTAAACCCGACTCCCTGGGTCGCGGTT‑TCACTATTACCAGACATTATTTTCGCCGCACCGCCATGAAAGCGCGTAACCACGCCttttt                                                                                   <  2:242542/251‑1 (MQ=255)                                                                                                                                                             cccgttctgcCTCAGTCCGGAACAATTTGAAAACAAGAACCTCTCTTAGGCCTGTGTCCATATGTCGTTGGTAGGATCAGGCA‑CCCTGTCGTGGAGCGTTTTG‑CTGGCCGCCTGCGCGATTCTGTTTTTGGGCGCCCTGGCCGGCTAAAACCACTCTTTAAACCCGCTTTCCTGGGGC‑CGGTTGTCTCTATTACCGGACTTCATTTTCGCCGCCCCGCCATGAAAGCGCGTAACCACGCCTTTTTGTTc                                                                               <  1:179179/241‑1 (MQ=16)                                                                                                                                                                    ggcCTCAGTCCGGAACAATTTGAAAACAAGAACCTCGCTTAGGCCTGTGTCCATATTACGTGGGTAGGATCAGTCATCCCT‑TCGTGGATCATTTTGACTG‑CCGCCTGCGCTATTCTGTTTTTTGGCGCGCTGGCGAGCTGAAATCGCTCTTTAAACCCGACTTCCTGGGTCTCGGTT‑TCACTATTACCAGACATTATTTTCGCCGCACCGCCATGAAAGCGCGTAACCACGCCTTTTTGTTCGAGAAAgcg                                                                      >  1:13304/1‑251 (MQ=255)                                                                                                                                                                     gcCTCAGTCCGGCACAATTTGCAAACAAGCACATCGCTTCGGCCTGTGTCCATATTACGTGGGTAGGATCAGTCATCCCT‑TCGTGGATCATTTTGACTG‑CCGCCTGCGCTATTCTGTTTTTTGGCGCGCTGGCGAGCTGAAATCGCTCTTTAAACCCGACTTCCTGGGTCTCGGTT‑TCACTATTACCAGACATTCTTTTCGCCGCACCGCCATGAAAGCGCGTAACCACGCCTTTTTGTTc                                                                               >  2:179179/1‑241 (MQ=255)                                                                                                                                                                                   cAATTTGAAAACAAGAACCGCGCTTAGTCCTGTGTCCATATTGCGTGTGTAGGATCAGTCATCCCT‑TCGTGGATCATTTTGTCTG‑CCCCCTGCGCTATTCGGTTTTTTGGCGCGATGGCGAGCTGAAATCGTTCTTTAAACCCGTCTTCCTGTGTCTCGGTT‑TCACTATTGCCAGACATTATTTTCGCGCCACCGCCATGAAAGCGCGTAACCACGCCTTTTTGTTCGAGAAAGCGCAAATCGGCACGGAt                                                       <  1:6749/251‑1 (MQ=255)                                                                                                                                                                                        tGAAAACAAGAACCTCGATTAAGCCTGTCTACCTATTACGTGGGTAGGATCAGTCATCCCT‑TCGTGGATAATTTTGACTG‑CCGCATGCGCTATTCTGTTTTTTGGCGCGCTGGCGAGCTGAAATCGCTATTTAACCCCGACTTCCTGGGTCTCGGTT‑TCACTATTACCAGACATTATTTTCGCCGCACCGCCATGAAAGCGCGTAACCCAGCCTTTTTGTTCGAGAAAGCGCAAATCGGCACGGATTGTCg                                                  >  2:135613/1‑251 (MQ=255)                                                                                                                                                                                                          ttAGGCCTGTGTCCATATTACGTGGGTAGGATCAGTCATCCCT‑TCGTGGATCATTTTGACTG‑CCGCCTGCGCTATTCTGTTTTTTGGCGCGCTGGCGAGCTGAAATCGCTCTTTAAACCCGACTTCCTGGGTCTCGGTT‑TCACTATTACCAGACATTATTTTCGCCGCACCGCCATGAAAGCGCGTAACCACGCCTTTTTGTTCGAGAAAGCGCAAATCGGCACGGATTGTCGCTTCCGAGGCAGCAAAt                                 >  2:65300/1‑250 (MQ=255)                                                                                                                                                                                                                                        aTCAGTCATCCCT‑TCGTGGATCATTTTGACTG‑CCGCCTGCGCTATTCTGTTTTTTGGCGCGCTGGCGAGCTGAAATCGCTCTTTAAACCCGACTTCCTGGGTCTCGGTT‑TCACTATTACCAGACATTATTTTCGCCGCACCGCCATGAAAGCGCGTAACCACGCCTTTTTGTTCGAGAAAGCGCAAATCGGCACGGATTGTCGCTTACGAGGCAGCAAATACTCCCGCCAGATCCTGAACAAGCACGGTTc  >  2:271393/1‑251 (MQ=255)                                                                                                                                                                                                                                           |                                                                                                                                                                                                                                                           AGGTTGCTGCTACGATAATGCCTGCGTGGAAAGCTTCTTTCATTCGCTGAAAGTGGAATGTATCCATGGAGAACACTTTATCAGCCGGGAAATAATGCGGGCAACGGTGTTTAATTATATCGAATGTGATTACAATCGGTGGCGGCGGCACAGTTGGTGTGGCGGCCTCAGTCCGGAACAATTTGAAAACAAGAACCTCGCTTAGGCCTGTGTCCATATTACGTGGGTAGGATCAGTCATCCCT‑TCGTGGATCATTTTGACTG‑CCGCCTGCGCTATTCTGTTTTTTGGCGCGCTGGCGAGCTGAAATCGCTCTTTAAACCCGACTTCCTGGGTCTCGGTT‑TCACTATTACCAGACATTATTTTCGCCGCACCGCCATGAAAGCGCGTAACCACGCCTTTTTGTTCGAGAAAGCGCAAATCGGCACGGATTGTCGCTTCCGAGGCAGCAAATACTCCCGCCAGATCCTGAACAAGCACGGTTC  >  NC_000913/2171194‑2171675

Alignment Legend
Aligned base mismatch/match (shaded by quality score): ATCG/ATCG < 3 ≤ ATCG/ATCG < 12 ≤ ATCG/ATCG < 14 ≤ ATCG/ATCG < 24 ≤ ATCG/ATCG < 38 ≤ 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.