Predicted mutation
evidence	seq id	position	mutation	annotation	gene	description
JC JC	NC_000913	1,291,151	IS5 (–) +4 bp	coding (910‑913/1014 nt)	rssB →	regulator of RpoS

New junction evidence
		seq id	position	reads (cov)	reads (cov)	score	skew	freq	annotation	gene	product
*	?	NC_000913	1291151 =	0 (0.000)	27 (1.020)	25/490	0.2	100%	coding (910/1014 nt)	rssB	regulator of RpoS
	?	NC_000913	= 2290113	NA (NA)					noncoding (1/1195 nt)	IS5	repeat region
*	?	NC_000913	= 1291154	0 (0.000)	13 (0.490)	12/488	0.8	100%	coding (913/1014 nt)	rssB	regulator of RpoS
	?	NC_000913	2101749 =	NA (NA)					noncoding (1195/1195 nt)	IS5	repeat region

GTATATCAGCACCCCGAAGGGGCTAAGTTCTGAAAAGGAGGCGAGTTAGCATAATTAAGACAATTACTTATACGAATGGCGACGATAGTACCACCAGCCGACATTAGCAGGTAATGCAAATTTAGCCCGCGTTATCGTTTGCTCATTCTGCAGACAACATCAAGCGCAGTCGACCACCGGTTCCCCATATTTGGCATTGCCAGGCATCGCATCGCTGGCTCAATTGATTCAAATAAGCGTTACCTAA‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑  <  NC_000913/1291397‑1291151 ‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑GGAAGGTGCGAACAAGTCCCTGATATGAGATCATGTTTGTCATCTGGAGCCATAGAACAGGGTTCATCATGAGTCATCAACTTACCTTCGCCGACAGTGAATTCAGCAGTAAGCGCCGTCAGACCAGAAAAGAGATTTTCTTGTCCCGCATGGAGCAGATTCTGCCATGGCAAAACATGGTGGAAGTCATCGAGCCGTTTTACCCCAAGGCTGGTAATGGCCGGCGACCTTATCCGCT  <  NC_000913/2290113‑2289876                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                       GTATATCAGCACCCCGAAGGGGCTAAGTTCTGAAAAGGAGGCGAGTTAGCATAATTAAGACAATTACTTATACGAATGGCGACGATAGTACCACCAGCCGACATTAGCAGGTAATGCAAATTTAGCCCGCGTTATCGTTTGCTCATTCTGCAGACAACATCAAGCGCAGTCGACCACCGGTTCCCCATATTTGGCATTGCCAGGCATCGCATCGCTGGCTCAATTGATTCAAATAAGCGTTACCTAAGGAA                                                                                                                                                                                                                                            <  1:189754/251‑1                     ggctacgaTCTGAAAAGGAGGCGCGTTAGCATACTTAAGACAATTACTTATACGACTGGCGACGATAGTACCACCAGCCGACATTAGCAGGTCCTGCAAATTTAGCCCGCGTTATCGTTTGCTCATTCTGCAGACAACATCAAGCGCAGTCGACCACCGGTTCCCCATATTTGGCATTGCACGGCATCGCATCGCTGGCTCAATTGATTCAAATAAGCGTTACCTAAGGAAGGTGCGAACAAGTCCCTGAT                                                                                                                                                                                                                        >  2:162256/9‑251                        TAAGTTCTGAAAAGGAGGCGAGTTAGCATAATTAAGACAATAACTTATACGAACGGCGAGGATAGTACCACCAGCCGCCATTAGCAGGTAATGCAAATTTAGCACGCGTTCTCGTTTGCTCTTTCTGCAGACAACATCAAGCGCAGTCGACCACCGGCTCCCCCTATTTGGCATTACCAGGCATCGCATCGCTGGCTCAATTGATTCACATAAGCGTTACCTAAGGAAGGTGCGAACAAGTCCCTGATATG                                                                                                                                                                                                                     >  2:164429/1‑251                           attcaGAAAAGGAGGCGAGTTAGCATAATTAAGACAATTACTTAGACGAATGGCGACGATAGTACCACAAACCGACATTAGCAGGTAATGCAAATTTAGCCCGCTTTATCGTTTGCTCATTCTGCAGACAACATCAAGCGCAGTCGATCACCGGTTCCCCATATTTGGCAGTGCCAGGCAGCGCAGCGCTGGCGCAGTTGATGCAAATAAGCGTTACCTAAGGAAGGTGGGAACAAGTCCCTGATATGAta                                                                                                                                                                                                                  <  2:205832/246‑3                                                        TAAGAAAATTCCTTATACGAATGGCGACGATAGTACCACCAGCCGACATTAGCAGGTAATGCAAATTTAGCCCGCGTTATCGTTTGCTCATTCTGCAGACAACATCAAGCGCAGTCGACCACCGGTTCCCCATATTTGGCATTGCCAGGCATCGCATCGCTGGCTCAATTGATTCAAATAAGCGTTACCTAAGGAAGGTGCGTACAAGTCCCTGATATGAGATCATGTTTGTCATCTGGAGCCATAGAAC                                                                                                                                                                                      >  1:84840/1‑250                                                                   CTTATACGAATGGCGACGATAGTACCACCAGCCGACATTAGCAGGTAATGCAAATTTAGCCCGCGTTATCGTTTGCTCATTCTGCAGACAACATCAAGCGCAGTCGACCACCGGTTCCCCATATTTGGCATTGCCAGGCATCGCATCGCTGGCTCAATTGATTCAAATAAGCGTTACCTAAGGAAGGTGCGAACAAGTCCCTGATATGAGATCATGTTTGTCATCTGGAGCCATAGAACAGGGTTCATCAT                                                                                                                                                                          >  2:55545/1‑251                                                                     TATACGAATGGCGACGATAGTACCACCAGCCGACATTAGCAGGTAATGCAAATTTAGCCCGCGTTATCGTTTGCTCATTCTGCAGACAACATCAAGCGCAGTCGACCACCGGTTCCCCATATTTGGCATTGCCAGGCATCGCATCGCTGGCTCAATTGATTCAAATAAGCGTTACCTAAGGAAGGTGCGAACAAGTCCCTGATATGAGATCATGTTTGTCATCTGGAGCCATAGAACAGGGTTTATCATG                                                                                                                                                                         <  2:164773/250‑1                                                                          GAATGGCGACGATAGTACCACCAGCCGACATTAGCAGGTAATGCAAATTTAGCCCGCGTTATCGTTTGCTCATTCTGCAGACAACATCAAGCGCAGTCGACCACCGGTTCCCCATATTTGGCATTGCCAGGCATCGCATCGCTGGCTCAATTGATTCAAATAAGCGTTACCTAAGGAAGGTGCGAACAAGTCCCTGATATGAGATCATGTTTGTCATCTGGAGCCATAGAACAGGGTTCATCATGAGTCAT                                                                                                                                                                   <  1:243733/251‑1                                                                                 GACGATAGTACCACCAGCCGACATTAGCAGGTAATGCAAATTTAGAACGAGTTATCGTTTGCTCATTCTGCAGAAAACATAAAGCGCAGTCGACCACCGGTTCCCCATATTTGGCATTGCAAGGCATCGCATCGCTGGCTCAATTGATTCAAATAAGCGTTAACTAAGGAAGGTGCGAACAAGTCCCTGATATGAGATCATGTTTGTCATATGGAGCCATAGAACAGGGTTCATCATGAGTCATCACCTT                                                                                                                                                             >  1:255791/1‑250                                                                                        GTACCACCAGCCGACATTAGCAGGTAATGCAAATTTAGCCCGCGTTATCGTTTGCTCATTCTGCAGACAACATCAAGCGCAGTCGACCACCGGTTCCCCATATTTGGCATTGCCAGGCATCGCATCGCTGGCTCAATTGATTCAAATAAGCGTTACCTAAGGAAGGTGCGAACAAGTCCCTGATATGAGATCATGTTTGTCATCTGGAGCCATAGAACAGGGTTCATCATGAGTCATCAACTTACCTTCGC                                                                                                                                                     <  1:189886/251‑1                                                                                                  CCGACATTAGCAGGTAATGCAAATTTAGCCCGCGTTATCGTTTGCTCATTCTGCAGACAACATCAAGCGCAGTCGACCACCGGTTCCCCATATTTGGCATTGCCAGGCATCGCATCGCTGGCTCAATTGATTCAAATAAGCGTTACCTAAGGAAGGTGCGAACAAGTCCCTGATATGAGATCATGTTTGTCATCTGGAGCCATAGAACAGGGTTCATCATGAGTCATCAACTTACCTTCGCTGACAGTGAA                                                                                                                                           <  1:94689/251‑1                                                                                                                                         GTTTGCTCATTCTGCAGACAACATCAAGCTCAGTAGACCACCGGTTCCCCATATTTGGCATTGCCAGGCATCGCATCGCTGGCTCAATTGATTCAAATAAGCGTTACCTAAGGAAGGTGCGAACAAGTCCCTGATATGAGATCATGTTTTTCATCTGGAGCCATAGAACAGGGTTCAGCATGAGTCATCAACTTACCTTCGCCGACAGTGAATTCAGCAGTAAGCGCCGTCATACCAGAAAAGAGATTTTC                                                                                                    <  1:206446/251‑1                                                                                                                                          TTTGCTCATTCTGCAGACAACATCAAGCGCAGTCGACCACCGGTTCCCCATATTTGGCATTGCCAGGCATCGCATCGCTGGCTCAATTGATTCAAATAAGCGTTACCTAAGGAAGGTGCGAACAAGTCCCTGATATGAGATCATGTTTGTCATCTGGAGCCATAGAACAGGGTTCATCATGAGTCATCAACTTACCTTCGCCGACAGTGAATTCAGCAGTAAGCGCCGTCAGACCAGAAAAGAGATTTTCT                                                                                                   >  1:132389/1‑251                                                                                                                                             GCTCATTCTGCAGACAACATCAAGCGCAGTCGACCACCGGTTCCCCATATTTGGCATTGCCAGGCCTCGCATCGCTGGCTCAATTGATTCAAATAAGCGTTACCTAAGGAAGGTGCGAACAAGTCCCTGATATGAGATCATGTTTGTCATCTGGAGCCATAGAACAGGGTTCATCATGAGTCATCAACTTACCTTCGCCGACAGTGAATTCAGCAGTAAGCGCCGTCAGACCAGAAAAGAGATTTTCTTGT                                                                                                >  2:121939/1‑251                                                                                                                                                CATTCTGCAGACAACATCAAGCGCAGTCGACCACCGGTTCCCCATATTTGGCATTGCCAGGCATCGCATCGCTGGCTCAATTGATTCAAATAAGCGTTACCTAAGGAAGGTGCGAACAAGTCCCTGATATGAGATCATGTTTGTCATCTGGAGCCATAGAACAGGGTTCATCATGAGTCATCAACTTACCTTCGCCGACAGTGAATTCAGCAGTAAGCGCCGTCAGACCAGAAAAGAGATTTTCTTGTC                                                                                               <  1:55545/249‑1                                                                                                                                                                      GCAGTCGACCACCGGTTCCCCATATTTGGCATTGCCAGGCATCGCATCGCTGGCTCAATTGATTCAAATAAGCGTTACCTAAGGAAGGTGCGAACAAGTCCCTGATATGAGATCATGTTTGTCATCTGGAGCCATAGAACAGGGTTCATCATGAGTCATCAACTTACCTTCGCCGACAGTGAATTCAGCAGTAAGCGCCGTCAGACCAGAAAAGAGATTTTCTTGTCCCGCATGGAGCAGATTCTGCCATG                                                                       <  1:99671/251‑1                                                                                                                                                                             ACCACCGGTTCCCCATATTTGGCATTGCCAGGCATCGCATCGCTGGCTCAATTGATTCAAATAAGCGTTACCTAAGGAAGGTGCGAACAAGTCCCTGATATGAGATCATGTTTGTCATCTGGAGCCATAGAACAGGGTTCATCATGAGTCATCAACTTACCTTCGCCGACAGTGAATTCAGCAGTAAGCGCCGTCAGACCAGAAAAGAGATTTTCTTGTCCCGCATGGAGCAGATTCTGCCATGGCAAAAC                                                                >  1:120475/1‑251                                                                                                                                                                                           ATATTTGGCATTGCCAGGCATCGCATCGCTGGCTCAATTGATTCAAATAAGCGTTACCTAAGGAAGGTGCGAACAAGTCCCTGATATGAGATCATGTTTGTCATCTGGAGCCATAGAACAGGGTTCATCATGAGTCATCAACTTACCTTCGCCGACAGTGAATTCAGCAGTAAGCGCCGTCAGACCAGAAAAGAGATTTTCTTGTCCCGCATGGAGCAGATTCTGCCATGGCAAAACATGGTGGAAGTCAT                                                  >  2:41533/1‑251                                                                                                                                                                                             ATTTGGCATTGCCAGGCATCGCATCGCTGGCTCAATTGATTCAAATAAGCGTTACCTAAGGAAGGTGCGAACAAGTCCCTGATATGAGATCATGTTTGTCATCTGGAGCCATAGAACAGGGTTCATCATGAGTCATCAACTTACCTTCGCCGACAGTGAATTCAGCAGTAAGCGCCGTCAGACCAGAAAAGAGATTTTCTTGTCCCGCATGGAGCAGATTCTGCCATGGCAAAACATGGTGGAAGTCATCG                                                >  1:168310/1‑251                                                                                                                                                                                              TTTGGCATTGCCAGGCATCGCATCGCTGGCTCAATTGATTCAAATAAGCGTTACCTATGGAAGGTGCGAACAAGTCCCTGATATGAGATCTTGTTTGTCATCTGGAGCCATAGAACAGGGTTCATCATGAGTCATAAACTTACCTTCGCCGACAGTGAATTCAGCAGTAAGCGCCGTCAGACCAGCAAAGAGATTTTCTTGTCCCGCATGGAGCAGATTCAGCCATGGCAAAACATGGCGGAcgcaatagg                                               >  2:197234/1‑242                                                                                                                                                                                                        CCAGGCATCGCATCGCTGGCTCAATTGATTCAAATAAGCGTTACCTAAGGAAGGTGCGAACAAGTCACTGATATGAGATCATGTTTGTCATCTGGAGCCATAGAACAGGGTTCATCATGAGTCATCAACTTACCTTCGCCGACA                                                                                                                                                >  1:249547/1‑144                                                                                                                                                                                                          AGGCATCGCATCGCTGGCTCAATTGATTCAAATAAGCGTTACCTAAGGAAGGTGCGAACAAGTCCCTGATATGAGATCATGTTTGTCATCTGGAGCCATAGAACAGGGTTCATCATGAGTCATCAACTTACCTTCGCCGACAGTGAATTCAGCAGTAAGCGCCGTCAGACCAGAAAAGAGATTTTCTTGTCCCGCATGGAGCAGATTCTGCCATGGCAAAACATGGTGGAAGTCATCGAGCCGTTTTACCC                                   >  1:119265/1‑251                                                                                                                                                                                                                         GGCTCAAGTGATTCAAATAAGCGTTACCTAAGGAAGGTGCGAACAAGTCCCTGATATGAGATCATGTTTGTCATCTGGAGCCATAGAACAGGGTTCATCATGAGTCATCAACTTACCTTCGCCGACAGTGAATTCAGCAGTAAGCGCCGTCAGACCAGAAAAGAGATTTTCTTGTCCCGCATGGAGCAGATTCTGCCATGGCAAAACATGGTGGAAGTCATCGAGCCGTTTTACCCCAAGGCTGGTAAT                      <  1:121939/249‑1                                                                                                                                                                                                                                    TTCAAATAAGCGTTACCTAAGGAAGGAGCGAACAAGTACCTGATATGAGATCATGTTTGTCATCTGAAGCCATAGAACAGGGTTCATCATGAGTCATCAACTTACCTTCGCCGACAGTGAATTCAGCAGTAAGCGCCGTCAGACCAGAACAGAGATTTTCTTGTCCCGCATGGAGCAGATTCTGACATGGCAACACATGGCGGAAGTCATCGAGCCGTTTTACACCAAGGCTGGTAATGGCCGGCGACCTT         >  1:164310/1‑251                                                                                                                                                                                                                                      CAAATAAGCGTTACCTAAGGAAGGTGCGAACAAGTCCCTGATATGAGATCATGTTTGTCATCTGGAGCCATAGAACAGGGTTCATCATGAGTCATCAACTTACCTTCGCCGCCAGTGAATTCAGCAGTAAGCGCCGTCAGACCAGAAAAGATATTTTCTTGTCCCGCATGGAGCAGATTCTGCCATGGCAAAACATGGTGGAAGTCATCGAGCCGTTTTACCCCAAGGCTGGTAATGGCCGGCGACCTTA        <  1:152164/250‑1                                                                                                                                                                                                                                       AAATAAGCGTTACCTAAGGAAGGTGCGAACAAGTCCCTGATATGAGATCATGTTTGTCATCTGGAGCCATAGAACAGGGTTCATCATGAGTCATCAACTTACCTTCGCCGACAGTGAATTCAGCAGTAAGCGCCGTCAGACCAGAAAAGAGATTTTCTTGTCCCGCATGGAGCAGATTCTGCCATGGCAAAACATGGTGGAAGTCATCGAGCCGTTTTACCCCAAGGCTGGTAATGGCCGGCGACCTTATC      <  2:168310/251‑1                                                                                                                                                                                                                                           AAGCGTTACCTAAGGAAGGTGCGAACAAGTCCCTGATATGAGATAATGTTTGTCATCTGGAGCCATAGAACAGGGTTCATCCTGAGTCATCACCTTACCTTCGCCGACAGCGAATTCAGCAGTAAGCGCCGTCAGACCAGAAAAGAGATTTTCTTGTCCCGCATGGAGCAGATTCTGCCATGGCAAAACATGGTGGAAGTCATCGAGCCGTTTTACACCAAGGCTGGTAATGGCCGGCGAACTTATCCGCT  >  1:129490/1‑251                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                       GTATATCAGCACCCCGAAGGGGCTAAGTTCTGAAAAGGAGGCGAGTTAGCATAATTAAGACAATTACTTATACGAATGGCGACGATAGTACCACCAGCCGACATTAGCAGGTAATGCAAATTTAGCCCGCGTTATCGTTTGCTCATTCTGCAGACAACATCAAGCGCAGTCGACCACCGGTTCCCCATATTTGGCATTGCCAGGCATCGCATCGCTGGCTCAATTGATTCAAATAAGCGTTACCTAA‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑  <  NC_000913/1291397‑1291151 ‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑GGAAGGTGCGAACAAGTCCCTGATATGAGATCATGTTTGTCATCTGGAGCCATAGAACAGGGTTCATCATGAGTCATCAACTTACCTTCGCCGACAGTGAATTCAGCAGTAAGCGCCGTCAGACCAGAAAAGAGATTTTCTTGTCCCGCATGGAGCAGATTCTGCCATGGCAAAACATGGTGGAAGTCATCGAGCCGTTTTACCCCAAGGCTGGTAATGGCCGGCGACCTTATCCGCT  <  NC_000913/2290113‑2289876

Alignment Legend
Aligned base mismatch/match (shaded by quality score): ATCG/ATCG < 3 ≤ ATCG/ATCG < 14 ≤ ATCG/ATCG < 15 ≤ ATCG/ATCG < 33 ≤ 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.