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

Missing coverage evidence...
			seq id	start	end	size	←reads	reads→	gene	description
*	*	÷	NC_000913	257908	258683	776	31 [1]	[0] 30	[crl]	[crl]

New junction evidence
		seq id	position	reads (cov)	reads (cov)	score	skew	freq	annotation	gene	product
*	?	NC_000913	= 257907	1 (0.030)	22 (0.820)	16/116	0.3	98.0%	intergenic (+8/‑769)	crl/crl	pseudogene, sigma factor‑binding protein, RNA polymerase holoenzyme formation stimulator;regulator; Surface structures; transcriptional regulator of cryptic csgA gene for curli surface fibers/pseudogene, sigma factor‑binding protein, RNA polymerase holoenzyme formation stimulator;regulator; Surface structures; transcriptional regulator of cryptic csgA gene for curli surface fibers
	?	NC_000913	258684 =	0 (0.000)					pseudogene (9/331 nt)	crl	pseudogene, sigma factor‑binding protein, RNA polymerase holoenzyme formation stimulator;regulator; Surface structures; transcriptional regulator of cryptic csgA gene for curli surface fibers

TGGACACCCGAAGAGCAGATTGATCAAAAAATTTACCGCACTAGGCCCGTATATTCGTGAAGGTAGGTAATGACTCCAACTTATTGATAGTGTTTTATGTTCAGATAATGCCCGATGACTTTGTCATGCAG  >  NC_000913/257843‑257973                                                                 |                                                                   tGGACACCCGAAGAGCAGATTGATCAAAAAATTTACCGCACTAGGCCCGTATATTCGTGAAGGTAagt                                                                 <  1:270898‑M1/68‑4 (MQ=255) tGGACACCCGAAGAGCAGATTGATCAAAAAATTTACCGCACTAGGCCCGTATATTCGCGAAGGTAagt                                                                 <  2:1048776‑M1/68‑4 (MQ=255) tGGACACACGTTGTGTAGATTGATAAAAAAATTTACCGCTCTAGTCCCGTATATTCTTGAatgtaagt                                                                 <  1:410258/68‑1 (MQ=255)  ggACACCCGAAGAGCAGATTGATCAAAAAATTTACCGCACTAGGCCCGTATATTCGTGAAGGTAagtg                                                                <  2:358948‑M1/68‑5 (MQ=255)  ggACACCCGAAGAGCAGATTGATCAAAAAATTTACCGCACTAGGCCCGTATATTCGTGAAGGTAagtg                                                                <  2:853142‑M1/68‑5 (MQ=255)       cccGAAGAGCAGATTGATCAAAAAATTTACCGCACTAGGCCCGTATATTCGTGAAGGTAagtgcaaag                                                           <  1:809121‑M1/68‑10 (MQ=255)              agCAGATTGATCAAAAAATTTACCGCACTAGGCCCGTATATTCGTGAAGGTAagtgcaaagataatcg                                                    >  1:913676‑M1/1‑52 (MQ=255)                cAGATTGATCAAAAAATTTACCGCACTAGGCCCGTATATTCGTGAAGGTAagtgcaaagataatcgat                                                  <  2:694588‑M1/68‑19 (MQ=255)                   aTTGATCAAAAAATTTACCGCACTAGGCCCGTATATTCGTGAAGGTAagagcaaagataatcgattct                                               <  1:1087159‑M1/68‑22 (MQ=255)                    ttGATCAAAAAATTTACCGCACTAGGCCCGTATATTCGTGATGGTAagtgcaaagataatcgattctt                                              <  1:1068898‑M1/68‑23 (MQ=255)                    ttGATCAAAAAATTTACCGCACTAGGCCCGTATATTCGTGAAGGTAagtgcaaagataatcgattctt                                              <  2:94427‑M1/68‑23 (MQ=255)                    ttGATCAAAAAATTTACCGCACTAGGCCCGTATATTCGTGAAGGTAagtgcaaagataatcgattctg                                              >  1:261098‑M1/1‑46 (MQ=255)                         cAAAAAATTTACCGCACTAGGCCCGTATATTCGTGAAGGTAagtgcaaagataatcgattctttttcg                                         >  2:650948‑M1/1‑41 (MQ=255)                             aaaTTTACCGCACTAGGCCCGTATATTCGTGAAGGTAagtgcaaagataatcgattctttttcgattg                                     >  2:362720‑M1/1‑37 (MQ=255)                              aaTCTACCGCACTAGGCCCGTATATTCGTGAAGGTAagtgcaaagataatcgcttctttttcgattgt                                    <  2:913673‑M1/68‑33 (MQ=255)                                ttaaccgCACTAGTCCCGTATATTCGTGAAGGTAagtgcaaagattatcgattctttttcgtttgtct                                  <  1:243702‑M1/65‑35 (MQ=255)                                    ccGCACTAGGCCCGTATATTCGTGAAGGTAagtgcaaagataatcgattctttttcgattgtctggct                              <  1:825158‑M1/68‑39 (MQ=255)                                    ccGCACTAGGCCCGTATATTCGTGAAGGTAagtgcaaagataatcgattctttttcgattgtctggct                              <  1:257805‑M1/68‑39 (MQ=255)                                        aCTAGGCCCGTATATTCGTGAAGGTAagtgcaaagataatcgattctttttcgattgtctggctgtat                          >  1:203958‑M1/1‑26 (MQ=255)                                              cccGTATATTCGTGAAGGTAagtgcaaagataatcgattctttttcgattgtctggctgtatgcgtca                    >  1:825400‑M1/1‑20 (MQ=255)                                              cccGTATATTCGTGAAGGTAagtgcaaagataatcgattctttttcgattgtctggctgtatgcgtca                    >  2:78318‑M1/1‑20 (MQ=255)                                                   atatTCGTGAAGGTAagtgcaaagataatcgattctttttcgattgtctggctgtatgcgtcaacgtg               >  1:1045751‑M1/1‑15 (MQ=255)                                                        cGTGAAGGTAagtgcaaagataatcgattctttttcgattgtctggctgtatgcgtcaacgtgaaacc          >  2:1134559‑M1/1‑10 (MQ=255)                                                           gAAGGTAagtgcaaagataatcgattctttttcgattgtctggctgtatgcg                       >  2:33233‑M1/1‑7 (MQ=255)                                                           gAAGGTAagtgcaaagataatcgattctttttcgattgtctggctgtatgcg                       <  1:33233‑M1/52‑46 (MQ=255)                                                            aaGGTAagtgcaaagataatcgattctttttcgattgtctggctgtatgcgtcaacgtgaaaccggca      <  2:305389‑M1/68‑63 (MQ=255)                                                            aaGGTAagtgcaaagataatcgattctttttcgattgtctggctgtatgcgtcaacgtgaaaccggca      <  1:362720‑M1/68‑63 (MQ=255)                                                            aaGGTAagtgcaaagataatcgattctttttcgattgtctggctgtatgcgtcaacgtgaaaccggca      <  1:103299‑M1/68‑63 (MQ=255)                                                             aGGTAagtgcaaagataatcgattctttttcgattgtctggctgtatgcgtcaacgtgaaaccggcac     >  2:770566‑M1/1‑5 (MQ=255)                                                              ggTAagtgcaaagataatcgattctttttcgattgtctggctgtatgcgtcaacgtgaaaccggcacc    >  2:866319‑M1/1‑4 (MQ=255)                                                                tAagtgcaaagataatcgattctttttcgattgtctggctgtatgcgtcaacgtgaaaccggcaccgg  >  2:956734‑M1/1‑2 (MQ=255)                                                                 |                                                                   TGGACACCCGAAGAGCAGATTGATCAAAAAATTTACCGCACTAGGCCCGTATATTCGTGAAGGTAGGTAATGACTCCAACTTATTGATAGTGTTTTATGTTCAGATAATGCCCGATGACTTTGTCATGCAG  >  NC_000913/257843‑257973

Alignment Legend
Aligned base mismatch/match (shaded by quality score): ATCG/ATCG < 3 ≤ ATCG/ATCG < 8 ≤ ATCG/ATCG < 13 ≤ ATCG/ATCG < 37 ≤ ATCG/ATCG
Unaligned base: atcg    Masked matching base: atcg    Alignment gap: ‑    Deleted base: ‑