Predicted mutation
evidence	seq id	position	mutation	annotation	gene	description
MC JC	NC_000913	1,978,503	Δ776 bp		insB‑5–insA‑5	insB‑5, insA‑5

Missing coverage evidence...
			seq id	start	end	size	←reads	reads→	gene	description
*	*	÷	NC_000913	1978503–1979270	1979278	9–776	69 [0]	[0] 68	insB‑5–insA‑5	insB‑5,insA‑5

New junction evidence
		seq id	position	reads (cov)	reads (cov)	score	skew	freq	annotation	gene	product
*	?	NC_000913	= 1978502	0 (0.000)	57 (1.470)	30/112	0.0	100%	intergenic (‑305/+16)	flhD/insB‑5	DNA‑binding transcriptional dual regulator FlhD/IS1 protein InsB
	?	NC_000913	1979279 =	0 (0.000)					intergenic (‑64/‑474)	insA‑5/uspC	IS1 protein InsA/universal stress protein C

TGGAGCACCTCAAAAACACCATCATACACTAAATCAGTAAGTTGGCAGCATCACCCATAAATGTATAAGTCATACTTTTGTTTTGGGTGTATTTCAATCTGTTAAAAAGTTTTTCGCTACGCTAGC  >  NC_000913/1979216‑1979341                                                                |                                                               gctgcgattttcaataatgcgtgatgcagatcacacaaaacactcaattacttaacataaatgta                                                               >  1:3188787‑M2/64‑65 (MQ=255) gctgcgattttcaataatgcgtgatgcagatcacacaaaacactcaattacttaacataaatgta                                                               >  1:2162448‑M2/64‑65 (MQ=255) gctgcgattttcaataatgcgtgatgcagatcacacaaaacactcaattacttaacataaatgta                                                               >  1:2149713‑M2/64‑65 (MQ=255)   tgcgattttcaataatgcgtgatgcagatcacacaaaacactcaattacttaacataaatgtata                                                             >  1:3236551‑M2/62‑65 (MQ=255)     cgattttcaataatgcgtgatgcagatcacacaaaacactcaattacttaacataaatgTATAAg                                                           <  1:1248302‑M2/6‑1 (MQ=255)     cgattttcaataatgcgtgatgcagatcacacaaaacactcaattacttaacataaatgTATAAg                                                           <  1:544259‑M2/6‑1 (MQ=255)      gattttcaataatgcgtgatgcagatcacacaaaacactcaattacttaacataaatgTATAAGt                                                          >  1:999211‑M2/59‑65 (MQ=255)      gattttcaataatgcgtgatgcagatcacacaaaacactcaattacttaacataaatgTATAAGt                                                          >  1:3291521‑M2/59‑65 (MQ=255)      gattttcaataatgcgtgatgcagatcacacaaaacactcaattacttaacataaatgTATAAGt                                                          >  1:2978940‑M2/59‑65 (MQ=255)              ataatgcgtgatgcagatcacacaaaacactcaattacttaacataaatgTATAAGTCATACttt                                                  >  1:3446256‑M2/51‑65 (MQ=255)              ataatgcgtgatgcagatcacacaaaacactcaattacttaacataaatgTATAAGTCATACttt                                                  >  1:3110071‑M2/51‑65 (MQ=255)                aatgcgtgatgcagatcacacaaagcactcaattacttaacataaatgTATAAGTCATACttttg                                                >  1:2533456‑M2/49‑65 (MQ=255)                aatgcgtgatgcagatcacacaaaacactcaattacttaacataaatgTATAAGTCATACttttg                                                >  1:2738529‑M2/49‑65 (MQ=255)                   gcgtgatgcagatcacacaaaacactcaattacttaacataaatgTATAAGTCATACttttgttt                                             >  1:2407961‑M2/46‑65 (MQ=255)                     gtgatgcagatcacacaaaacactcaattacttaacataaatgTATAAGTCATACttttgttttg                                           >  1:386202‑M2/44‑65 (MQ=255)                      tgatgcagatcacacaaaacactcaattacttaacataaatgTATAAGTCATACTTTTGTTTTgg                                          <  1:1890970‑M2/23‑1 (MQ=255)                       gatgcagatcacacaaaacactcaattacttaacataaatgTATAAGTCATACTTTTGTTTTggg                                         >  1:1995668‑M2/42‑65 (MQ=255)                        atgcagatcacacaaaacactcaattacttaacataaatgTATAAGTCATACTTTTGTTTTGGgt                                        <  1:1186801‑M2/25‑1 (MQ=255)                        atgcagatcacacaaaacactcaattacttaacataaatgTATAAGTCATACTTTTGTTTTGGgt                                        <  1:2746604‑M2/25‑1 (MQ=255)                        atgcagatcacacaaaacactcaattacttaacataaatgTATAAGTCATACTTTTGTTTTGGgt                                        <  1:57255‑M2/25‑1 (MQ=255)                         tgcagatcacacaaaacactcaattacttaacataaatgTATAAGTCATACTTTTGTTTTGGgtg                                       >  1:3627996‑M2/40‑65 (MQ=255)                          gcagatcacacaaaacactcaattacttaacataaatgTATAAGTCATACTTTTGTTTTGGgtgt                                      <  1:748563‑M2/27‑1 (MQ=255)                          gcagatcacacaaaacactcaattacttaacataaatgTATAAGTCATACTTTTGTTTTGGgtgt                                      >  1:732035‑M2/39‑65 (MQ=255)                           cagatcacacaaaacactcaattacttaacataaatgTATAAGTCATACTTTTGTTTTGGGTGTa                                     <  1:3124748‑M2/28‑1 (MQ=255)                            agatcacacaaaacactcaattacttaacataaatgTATAAGTCATCCTTTTGTTTTGGGTGTAt                                    <  1:3329509‑M2/29‑1 (MQ=255)                            agatcacacaaaacactcaattacttaacataaatgTATAAGTCATACTTTTGTTTTGGGTGTAt                                    <  1:3060024‑M2/29‑1 (MQ=255)                            agatcacacaaaacactcaattacttaacataaatgTATAAGTCATACTTTTGTTTTGGGTGTAt                                    >  1:1258001‑M2/37‑65 (MQ=255)                            agatcacacaaaacactcaattacttaacataaatgTATAAGTCATACTTTTGTTTTGGGTGTAt                                    <  1:379447‑M2/29‑1 (MQ=255)                               tcacacaaaacactcaattacttaacataaatgTATAAGTCATACTTTTGTTTTGGGTGTATTTc                                 >  1:1477007‑M2/34‑65 (MQ=255)                               tcacacaaaacactcaattacttaacataaatgTATAAGTCATACTTTTGTTTTGGGTGTATTTc                                 >  1:311333‑M2/34‑65 (MQ=255)                               tcacacaaaacactcaattacttaacataaatgTATAAGTCATACTTTTGTTTTGGGTGTATTTc                                 >  1:1610230‑M2/34‑65 (MQ=255)                               tcacacaaaacactcaattacttaacataaatgTATAAGTCATACTTTTGTTTTGGGTGTATTTc                                 >  1:2926090‑M2/34‑65 (MQ=255)                               tcacacaaaacactcaattacttaacataaatgTATAAGTCATACTTTTGTTTTGGGTGTATTTc                                 >  1:3581688‑M2/34‑65 (MQ=255)                               tcacacaaaacactcaattacttaacataaatgTATAAGTCATACTTTTGTTTTGGGTGTATTTc                                 >  1:2764228‑M2/34‑65 (MQ=255)                               tcacacaaaacactcaattacttaacataaatgTATAAGTCATACTTTTGTTTTGGGTGTATTTc                                 >  1:2085845‑M2/34‑65 (MQ=255)                               tcacacaaaacactcaattacttaacataaatgTATAAGTCATACTTTTGTTTTGGGTGTATTTc                                 >  1:1848823‑M2/34‑65 (MQ=255)                                    caaaacactcaattacttaacataaatgTATAAGTCATACTTTTGTTTTGGGTGTATTTCAATCt                            >  1:1645500‑M2/29‑65 (MQ=255)                                    caaaacactcaattacttaacataaatgTATAAGTCATACTCTTGTTTTGGGTGTATTTCAAtcc                            >  1:2409676‑M2/29‑64 (MQ=255)                                      aaacactcaattacttaacataaatgTATAAGTCATACTTTTGTTTTGGGTGTATTTCAATCTGt                          >  1:2461372‑M2/27‑65 (MQ=255)                                      aaacactcaattacttaacataaatgTATAAGTCATACTTTTGTTTTGGGTGTATTTCAATCTGt                          <  1:1540441‑M2/39‑1 (MQ=255)                                        acactcaattacttaacataaatgTATAAGTCATACTTTTGTTTTGGGTGTATTTCAATCTGTTa                        >  1:3341656‑M2/25‑65 (MQ=255)                                        acactcaattacttaacataaatgTATAAGTCATACTTTTGTTTTGGGTGTATTTCAATCTGTTa                        >  1:1891325‑M2/25‑65 (MQ=255)                                           ctcaattacttaacataaatgTATAAGTCATACTTTTGTTTTGGGTGTATTTCAATCTGTTaaaa                     >  1:774396‑M2/22‑65 (MQ=255)                                             caattacttaacataaatgTATAAGTCATACTTTTGTTTTGGGTGTATTTCAATCTGTTAAAAAg                   >  1:283649‑M2/20‑65 (MQ=255)                                              aattacttaacataaatgTATAAGTCATACTTTTGTTTTGGGTGTATTTCAATCTGTTAAAAAGt                  <  1:655692‑M2/47‑1 (MQ=255)                                               attacttaacataaatgTATAAGTCATACTTTTGTTTTGGGTGTATTTCAATCTGTTAAAAAGtt                 >  1:320542‑M2/18‑65 (MQ=255)                                               attacttaacataaatgTATAAGTCATACTTTTGTTTTGGGTGTATTTCAATCTGTTAAAAAGtt                 >  1:2325339‑M2/18‑65 (MQ=255)                                               attacttaacataaatgTATAAGTCATACTTTTGTTTTGGGTGTATTTCAATCTGTTAAAAAGtt                 >  1:197575‑M2/18‑65 (MQ=255)                                                  acttaacataaatgTATAAGTCATACTTTTGTTTTGGGTGTATTTCAATCTGTTAAAAAGttttt              >  1:615796‑M2/15‑65 (MQ=255)                                                  acttaacataaatgTATAAGTCATACTTTTGTTTTGGGTGTATTTCAATCTGTTAAAAAGttttt              >  1:2900946‑M2/15‑65 (MQ=255)                                                  acttaacataaatgTATAAGTCATACTTTTGTTTTGGGCGTATTTCAATCTGTTAAAAAGttttt              >  1:1204374‑M2/15‑65 (MQ=255)                                                    ttaacataaatgTATAAGTCATACTTTTGTTTTGGGTGTATTTCAATCTGTTAAAAAGTTTTTcg            >  1:554679‑M2/13‑65 (MQ=255)                                                    ttaacataaatgTATAAGTCATACTTTTGTTTTGGGTGTATTTCAATCTGTTAAAAAGTTTTTcg            >  1:1901849‑M2/13‑65 (MQ=255)                                                    ttaacataaatgTATAAGTCATACTTTTGTTTTGGGTGTATTTCAATCTGTTAAAAAGTTTTTcg            >  1:3132042‑M2/13‑65 (MQ=255)                                                      gacataaatgTATAAGTCATACTTTTGTTTTGGGTGTATTTCAATCTGTTAAAAAGTTTTTcgct          <  1:3520905‑M2/55‑1 (MQ=255)                                                      aacataaatgTATAAGTCATACTTTTGTTTTGGGTGTATTTCAATCTGTTAAAAAGTTTTTcgct          >  1:2662928‑M2/11‑65 (MQ=255)                                                      aacataaatgTATAAGTCATACTTTTGTTTTGGGTGTATTTCAATCTGTTAAAAAGTTTTTcgct          <  1:1591232‑M2/55‑1 (MQ=255)                                                        cataaatgTATAAGTCATACTTTTGTTTTGGGTGTATTTCAATCTGTTAAAAAGTTTTTcgctac        <  1:44895‑M2/57‑1 (MQ=255)                                                         ataaatgTATAAGTCATACTTTTGTTTTGGGTGTATTTCAATCTGTTAAAAAGTTTTTcgctacg       >  1:3472685‑M2/8‑65 (MQ=255)                                                         ataaatgTATAAGTCATACTTTTGTTTTGGGTGTATTTCAATCTGTTAAAAAGTTTTTcgctacg       >  1:3230667‑M2/8‑65 (MQ=255)                                                          taaatgTATAAGTCATACTTTTGTTTTGGGTGTATTTCAATCTGTTAAAAAGTTTTTcgctacgc      <  1:1638268‑M2/59‑1 (MQ=255)                                                           aaatgTATAAGTCATACTTTTGTTTTGGGTGTATTTCAATCTGTTAAAAAGTTTTTcgctacgct     <  1:1959152‑M2/60‑1 (MQ=255)                                                             atgTATAAGTCATACTTTTGTTTTGGGTGTATTTCAATCTGTTAAAAAGTTTTTCGCTACGCTAg   <  1:2154984‑M2/62‑1 (MQ=255)                                                              tgTATAAGTCATACTTTTGTTTTGGGTGTATTTCAATCTGTTAAAAAGTTTTTCGCTACGCTAGc  >  1:2836067‑M2/3‑65 (MQ=255)                                                              tgTATAAGTCATACTTTTGTTTTGGGTGTATTTCAATCTGTTAAAAAGTTTTTCGCTACGCTAGc  >  1:515143‑M2/3‑65 (MQ=255)                                                              tgTATAAGTCATACTTTTGTTTTGGGTGTATTTCAATCTGTTAAAAAGTTTTTCGCTACGCTAGc  >  1:2511922‑M2/3‑65 (MQ=255)                                                              tgTATAAGTCATACTTTTGTTTTGGGTGTATTTCAATCTGTTAAAAAGTTTTTCGCTACGCTAGc  >  1:2080159‑M2/3‑65 (MQ=255)                                                              tgTATAAGTCATACTTTTGTTTTGGGTGTATTTCAATCTGTTAAAAAGTTTTTCGCTACGCTAGc  >  1:92368‑M2/3‑65 (MQ=255)                                                                |                                                               TGGAGCACCTCAAAAACACCATCATACACTAAATCAGTAAGTTGGCAGCATCACCCATAAATGTATAAGTCATACTTTTGTTTTGGGTGTATTTCAATCTGTTAAAAAGTTTTTCGCTACGCTAGC  >  NC_000913/1979216‑1979341

Alignment Legend
Aligned base mismatch/match (shaded by quality score): ATCG/ATCG < 3 ≤ ATCG/ATCG < 15 ≤ ATCG/ATCG < 27 ≤ ATCG/ATCG < 32 ≤ ATCG/ATCG < 34 ≤ ATCG/ATCG
Unaligned base: atcg    Masked matching base: atcg    Alignment gap: ‑    Deleted base: ‑