Predicted mutation
evidence	seq id	position	mutation	annotation	gene	description
MC JC	NC_000913	257,908	Δ776 bp		insB9–[crl]	insB9, insA9, [crl]

Missing coverage evidence...
			seq id	start	end	size	←reads	reads→	gene	description
*	*	÷	NC_000913	257908–258674	258683	10–776	73 [0]	[0] 73	insB9–[crl]	insB9,insA9,[crl]

New junction evidence
		seq id	position	reads (cov)	reads (cov)	score	skew	freq	annotation	gene	product
*	?	NC_000913	= 257907	0 (0.000)	68 (1.450)	23/118	0.2	100%	intergenic (+8/+16)	crl/insB9	RNA polymerase holoenzyme assembly factor Crl/IS1 transposase B
	?	NC_000913	258684 =	0 (0.000)					pseudogene (9/331 nt)	crl	RNA polymerase holoenzyme assembly factor Crl

TGGACACCCGAAGAGCAGATTGATCAAAAAATTTACCGCACTAGGCCCGTATATTCGTGAAGGTAGGTAATGACTCCAACTTATTGATAGTGTTTTATGTTCAGATAATGCCCGATGACTTTGTCATGCAG  >  NC_000913/257843‑257973                                                                 |                                                                   tGGACACCCGAAGAGCAGATTGATCAAAAAATTTACCGCACTAGGCCCGTATATTCGTGAAGGTAagt                                                                 <  1:1062594‑M1/68‑4 (MQ=255) tGGACACCCGAAGAGCAGATTGATCAAAAAATTTACCGCACTAGGCCCGTATATTCGTGAAGGTAagt                                                                 <  1:365099‑M1/68‑4 (MQ=255) tGGACACCCGAAGAGCAGATTGATCAAAAAATTTACCGCACTAGGCCCGTATATTCGTGAAGGTAagt                                                                 <  1:2074447‑M1/68‑4 (MQ=255) tGGACACCCGAAGAGCAGATTGATCAAAAAATTTACCGCACTAGGCCCGTATATTCGTGAAGGTAagt                                                                 <  1:2074228‑M1/68‑4 (MQ=255) tGGACACCCGAAGAGCAGATTGATCAAAAAATTTACCGCACTAGGCCCGTATATTCGTGAAGGTAagt                                                                 <  1:1828587‑M1/68‑4 (MQ=255) tGGACACCCGAAGAGCAGATTGATCAAAAAATTTACCGCACTAGGCCCGTATATTCGTGAAGGTAagt                                                                 <  1:1403374‑M1/68‑4 (MQ=255) tGGACACCCGAAGAGCAGATTGATCAAAAAATTTACCGCACTAGGCCCGTATATTCGTGAAGGTAagt                                                                 <  1:82492‑M1/68‑4 (MQ=255) tGGACACCCGAAGAGCAGATTGATCAAAAAATTTACCGCACTAGGCCCGTATATTCGTGAAGGTAagt                                                                 <  1:983760‑M1/68‑4 (MQ=255) tGGACACCCGAAGAGCAGATTGATCAAAAAATTTACCGCACTAGGCCCGTATATTCGTGAAGGTAagt                                                                 <  1:910825‑M1/68‑4 (MQ=255) tGGACACCCGAAGAGCAGATTGAGCAAAAAATTTACCGCACTAGGCCCGTATATTCGTGAAGGTAagt                                                                 <  1:184134‑M1/68‑4 (MQ=255)  ggACACCCGAAGAGCAGATTGATCAAAAAATTTACCGCACTAGGCCCGTATATTCGTGAAGGTAagtg                                                                >  1:1343692‑M1/1‑64 (MQ=255)  ggACACCCGAAGAGCAGATTGATCAAAAAATTTACCGCACTAGGCCCGTATATTCGTGAAGGTAagtg                                                                <  1:2537718‑M1/68‑5 (MQ=255)  ggACACCCGAAGAGCAGATTGATCAAAAAATTTACCGCACTAGGCCCGTATATTCGTGAAGGTAagtg                                                                >  1:1164725‑M1/1‑64 (MQ=255)  ggACACCCGAAGAGCAGATTGATCAAAAAATTTACCGCACTAGGCCCGTATATTCGTGAAGGTAagtg                                                                <  1:3910368‑M1/68‑5 (MQ=255)  ggACACCCGAAGAGCAGATTGATCAAAAAATTTACCGCACTAGGCCCGTATATTCGTGAAGGTAagtg                                                                >  1:2015761‑M1/1‑64 (MQ=255)       cccGAAGAGCAGATTGATCAAAAAATTTACCGCACTAGGCCCGTATATTCGTGAAGGTAagtgcaaag                                                           >  1:3643820‑M1/1‑59 (MQ=255)        ccGAAGAGCAGATTGATCAAAAAATTTACCGCACCAGGCCCGTATATTCGTGAAGGTAagtgcaaaga                                                          <  1:2922256‑M1/68‑11 (MQ=255)         cGAAGAGCAGATTGATCAAAAAATTTACCGCACTAGGCCCGTATATTCGTGAAGGTAagtgcaaagat                                                         <  1:3344892‑M1/68‑12 (MQ=255)          gAAGAGCAGATTGATCAAAAAATTTACCGCACTAGGCCCGTATATTCGTGAAGGTAagtgcaaagata                                                        >  1:305328‑M1/1‑56 (MQ=255)            agagCAGATTGATCAAAAAATTTACCGCACTAGGCCCGTATATTCGTGAAGGTAagtgcaacgataat                                                      >  1:3891485‑M1/1‑54 (MQ=255)            agagCAGATTGATCAAAAAATTTACCGCACTAGGCCCGTATATTCGTGAAGGTAagtgcaaagataat                                                      <  1:684128‑M1/68‑15 (MQ=255)              agCAGATTGATCAAAAAATTTACCGCACTAGGCCCTTATATTCGTGAAGGTAagtgcaaagataatcg                                                    >  1:2725303‑M1/1‑52 (MQ=255)              agCAGATTGATCAAAAAATTTACCGCACTAGGCCCGTATATTCGTGAAGGTAagtgcaaagataatcg                                                    >  1:1766008‑M1/1‑52 (MQ=255)              agCAGATTGATCAAAAAATTTACCGCACTAGGCCCGTATATTCGTGAAGGTAagtgcaaagataatcg                                                    >  1:584948‑M1/1‑52 (MQ=255)              agCAGATTGATCAAAAAATTTACCGCACTAGGCCCGTATATTCGTGAAGGTAagtgcaaagataatcg                                                    >  1:2190239‑M1/1‑52 (MQ=255)              agCAGATTGATCAAAAAATTTACCGCACTAGGCCCGTATATTCGTGAAGGTAagtgcaaagataatcg                                                    >  1:2205171‑M1/1‑52 (MQ=255)              agCAGATTGATCAAAAAATTTACCGCACTAGGCCCGTATATTCGTGAAGGTAagtgcaaagataatcg                                                    >  1:2838144‑M1/1‑52 (MQ=255)              agCAGATTGATCAAAAAATTTACCGCACTAGGCCCGTATATTCGTGAAGGTAagtgcaaagataatcg                                                    >  1:2729151‑M1/1‑52 (MQ=255)              agCAGATTGATCAAAAAATTTACCGCACTAGGCCCATATATTCGTGAAGGTAagtgcaaagataatcg                                                    >  1:2747589‑M1/1‑52 (MQ=255)                  gATTGATCAAAAAATTTACCGCACTAGGCCCGTATATTCGTGAAGGTAagtgcaaagataatcgattc                                                >  1:2877216‑M1/1‑48 (MQ=255)                              aagttaccGCACTAGGCCCGTATATTCGTGAAGGTAagtgcaaagataatcgattctttttcgattgt                                    <  1:3779500‑M1/65‑33 (MQ=255)                              aaTTTACCGCACTAGGCCCGTATATTCGTGAAGGTAagtgcaaagataatcgattctttttcgattgt                                    <  1:3529176‑M1/68‑33 (MQ=255)                              aaTTTACCGCACTAGGCCCGTATATTCGTGAAGGTAagtgcaaagataatcgattctttttcgattgt                                    <  1:2996994‑M1/68‑33 (MQ=255)                              aaTTTACCGCACTAGGCCCGTATATTCGTGAAGGTAagtgcaaagataatcgattctttttcgattgt                                    <  1:593925‑M1/68‑33 (MQ=255)                              aaTTTACCGCACTAGGCCCGTATATTCGTGAAGGTAagtgcaaagataatcgattctttttcgattgt                                    <  1:3552033‑M1/68‑33 (MQ=255)                              aaTTTACCGCACTAGGCCCGTATATTCGTGAAGGTAagtgcaaagataatcgattctttttcgattgt                                    <  1:2384186‑M1/68‑33 (MQ=255)                              aaTTTACCGCACTAGGCCCGTATATTCGTGAAGGTAagtgcaaagataatcgattctttttcgattgt                                    <  1:1738849‑M1/68‑33 (MQ=255)                                  tACCGCACTAGGCCCGTATATTCGTGAAGGTAagtgcaaagataatcgattctttttcgattgtctgg                                <  1:620724‑M1/68‑37 (MQ=255)                                  tACCGCACTAGGCCCGTATATTCGTGAAGGTAagtgcaaagataatcgattctttttcgattgtctgg                                <  1:2700766‑M1/68‑37 (MQ=255)                                  tACCGCACTAGGCCCGTATATTCGTGAAGGTAagtgcaaagataatcgattctttttcgattgtctgg                                <  1:2789104‑M1/68‑37 (MQ=255)                                  tACCGCACTAGGCCCGTATATTCGTGAAGGTAagtgcaaagataatcgattctttttcgattgtctgg                                <  1:1335659‑M1/68‑37 (MQ=255)                                    ccGCACTAGGCCCGTATATTCGTGAAGGTAagtgcaaagataatcgattctttttcgattgtctggct                              <  1:984218‑M1/68‑39 (MQ=255)                                      gCACTAGGCCCGTATATTCGTGAAGGTAagtgcaaagataatcgattctttttcgattgtctggctgt                            <  1:52993‑M1/68‑41 (MQ=255)                                      gCACTAGGCCCGTATATTCGTGAAGGTAagtgcaaagataatcgattctttttcgattgtctggctgt                            <  1:1423156‑M1/68‑41 (MQ=255)                                      gCACTAGGCCCGTATATTCGTGAAGGTAagtgcaaagataatcgattctttttcgattgtctggctgt                            <  1:1180931‑M1/68‑41 (MQ=255)                                      gCACTAGGCCCGTATATTCGTGAAGGTAagtgcaaagataatcgattctttttcgattgtctggctgt                            <  1:336465‑M1/68‑41 (MQ=255)                                      gCACTAGGCCCGTATATTCGTGAAGGTAagtgcaaagataatcgattctttttcgattgtctggctgt                            <  1:3905520‑M1/68‑41 (MQ=255)                                      gCACTAGGCCCGTATATTCGTGAAGGTAagtgcaaagataatcgattctttttcgattgtctggctgt                            <  1:3896601‑M1/68‑41 (MQ=255)                                      gCACTAGGCCCGTATATTCGTGAAGGTAagtgcaaagataatcgattctttttcgattgtctggctgt                            <  1:218486‑M1/68‑41 (MQ=255)                                      gCACTAGGCCCGTATATTCGTGAAGGTAagtgcaaagataatcgattctttttcgattgtctggctgt                            <  1:3709518‑M1/68‑41 (MQ=255)                                          tAGGCCCGTATATTCGTGAAGGTAagtgcaaagataatcgattctttttcgattgtctggctgtatgc                        <  1:121912‑M1/68‑45 (MQ=255)                                              cccGTATATTCGTGAAGGTAagtgcaaagataatcgattctttttcgattgtctggctgtatgcgtcc                    >  1:1174528‑M1/1‑20 (MQ=255)                                              cccGTATATTCGTGAAGGTAagtgcaaagataatcgattctttttcgattgtctggctgtatgcgtca                    >  1:3045885‑M1/1‑20 (MQ=255)                                              cccGTATATTCGTGAAGGTAagtgcaaagataatcgattctttttcgattgtctggctgtatgcgtca                    >  1:1780248‑M1/1‑20 (MQ=255)                                              cccGTATATTCGTGAAGGTAagtgcaaagataatcgattctttttcgattgtctggctgtatgcgtca                    >  1:3776047‑M1/1‑20 (MQ=255)                                              cccGTATATTCGTGAAGGTAagtgcaaagataatcgattctttttcgattgtctggctgtatgcgtca                    >  1:355844‑M1/1‑20 (MQ=255)                                              cccGTATATTCGTGAAGGTAagtgcaaagataatcgattctttttcgattgtctggctgtatgcgtca                    >  1:328794‑M1/1‑20 (MQ=255)                                              cccGTATATTCGTGAAGGGAagtgcaaagataatcgattctttttcgattgtctggctgtatgcgtca                    >  1:745683‑M1/1‑20 (MQ=255)                                                cGTATATTCGTGAAGGTAagtgcaaagataatcgattctttttcgattgtctggctgtatgcgtcaac                  <  1:2275655‑M1/68‑51 (MQ=255)                                                cGTATATTCGTGAAGGTAagtgcaaagataatcgattctttttcgattgtctggctgtatgcgtcaac                  <  1:1348980‑M1/68‑51 (MQ=255)                                                cGTATATTCGTGAAGGTAagtgcaaagataatcgattctttttcgattgtctggctgtatgcgtcaac                  <  1:1808009‑M1/68‑51 (MQ=255)                                                 gtgtattcgTGAAGGTAagtgcaaagataatcgattctttttcgattgtctggctgtatgcgtcaacg                 <  1:3467752‑M1/65‑52 (MQ=255)                                                 gTATATTCGTGAAGGTAagtgcaaagataatcgattctttttcgattgtctggctgtatgcgtcaacg                 <  1:2423185‑M1/68‑52 (MQ=255)                                                  tataTTCGTGAAGGTAagtgcaaagataatcgattctttttcgattgtctggctgtatgcgtcaacgt                >  1:110551‑M1/1‑16 (MQ=255)                                                     atTCGTGAAGGTAagtgcaaagataatcgattctttttcgagtgtctggctgtatgcgtcaacgtgaa             >  1:3272558‑M1/1‑13 (MQ=255)                                                       tCGTGAAGGTAagtgcaaagataatcgattctttttcgattgtctggctgtatgcgtcaacgtgaaac           >  1:3948148‑M1/1‑11 (MQ=255)                                                        cGTGAAGGTAagtgcaaagataatcgattctttttcgattgtctggctgtatgcgtcaacgtgaaacc          >  1:1759411‑M1/1‑10 (MQ=255)                                                        cGTGAAGGTAagtgcaaagataatcgattctttttcgattgtctggctgtatgcgtcaacgtgaaacc          >  1:2277256‑M1/1‑10 (MQ=255)                                                            aaGGTAagtgcaaagataatcgattctttttcgattgtctggctgtatgcgtcaacgtgaaaccggca      <  1:2690064‑M1/68‑63 (MQ=255)                                                              ggTAagtgcaaagataatcgattctttttcgattgtctggctgtatgcgtcaacgtgaaaccggcacc    <  1:1554577‑M1/68‑65 (MQ=255)                                                              ggTAagtgcaaagataatcgattctttttcgattgtctggctgtatgcgtcaacgtgaaaccggcacc    <  1:300717‑M1/68‑65 (MQ=255)                                                               gTAagtgcaaagataatcgattctttttcgattgtctggctgtatgcgtcaacgtgaaaccggcaccg   >  1:2725036‑M1/1‑3 (MQ=255)                                                                tAagtgcaaagataatcgattctttttcgattgtctggctgtatgcgtcaacgtgaaaccggcaccgg  <  1:3291286‑M1/68‑67 (MQ=255)                                                                 |                                                                   TGGACACCCGAAGAGCAGATTGATCAAAAAATTTACCGCACTAGGCCCGTATATTCGTGAAGGTAGGTAATGACTCCAACTTATTGATAGTGTTTTATGTTCAGATAATGCCCGATGACTTTGTCATGCAG  >  NC_000913/257843‑257973

Alignment Legend
Aligned base mismatch/match (shaded by quality score): ATCG/ATCG < 3 ≤ ATCG/ATCG < 16 ≤ ATCG/ATCG < 25 ≤ ATCG/ATCG < 32 ≤ ATCG/ATCG < 34 ≤ ATCG/ATCG
Unaligned base: atcg    Masked matching base: atcg    Alignment gap: ‑    Deleted base: ‑