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	257908–258675	258683	9–776	32 [0]	[0] 32	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)	31 (1.020)	27/238	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

AATTTTGCCAATTTGGTAAAACAGTTGCATCACAACAGGAGATAGCAATGACGTTACCGAGTGGACACCCGAAGAGCAGATTGATCAAAAAATTTACCGCACTAGGCCCGTATATTCGTGAAGGTAGGTAATGACTCCAACTTATTGATAGTGTTTTATGTTCAGATAATGCCCGATGACTTTGTCATGCAGCTCCACCGATTTTGAGAACGACAGCGACTTCCGTCCCAGCCGTGCCAGGTGCTGC  >  NC_000913/257782‑258028                                                                                                                              |                                                                                                                          aaTTTTGCCAATTTGGTAAAACAGTTGCATCACAACAGGAGATAGCAATGACGTTACCGAGTGGACACCCGAAGAGCAGATTGATCAAAAAATTTACCGCACTAGGCACGCATATTCGTGAAGGTAagt                                                                                                                        >  2:452228‑M1/1‑126 (MQ=255)             ttGGTAAAACAGTTGCATAACAACAGGAGATAGCAATGACGTTACCGAGTGGACACCCAAAGAGCAGATTGATCAAAAAATTTAACGCCCTAGGCCCGTCTATTTGTGAAGGTAagtgcaaagataata                                                                                                            >  2:48662‑M1/1‑114 (MQ=255)              tgataaaACAGTTGCATCACAACAGGAGATAGCAATGACGTTACCGAGTGGACACCCGAAGAGCAGATTTATCAAAAAATTTTTCTTACTATTCTCTTATATTCGTGAAGGAAagtgcaaagataatcg                                                                                                           <  1:563254‑M1/126‑17 (MQ=255)                 tAAAACAGTTGCATCCCACCAGGAGATAGCAATAACGTTACAGAGAGGACACCCGAAGAGCAGATTGATCAAAAAATTTACCGCACTAGGCCCGTATATTCGTGAAGGTAagtgcaaagataatcgatt                                                                                                        >  1:619040‑M1/1‑110 (MQ=255)                     ccaGTAGCATCACAACAGGAGATAGCAATTACGTTACCGAGTGGACACCCGAAGAGCAGATTGATCAAAAAATTTACCGCACTAGGCCCGTATATTCGTGAAGGTAagtgcaaagataatcgagtcttt                                                                                                    <  1:437692‑M1/128‑24 (MQ=255)                         ttGCATCACAACAGGAGATAGCAATGACGTTACCGAGTGGACACCCGAAGAGCAGATTGATCAAAAAATTTACCGCACTAGGCCCGTATATTCGTGAAGGTAagtgcaaagataatcgattctttttcg                                                                                                >  2:344003‑M1/1‑102 (MQ=255)                                          aTAGCAATGACGTTACCGAGTGGACACCCGAAGAGCAGATTGATCAAAAAATTTACCGCACTAGGCCCGTATATTCGTGAAGGTAagtgcaaagataatcgattctttttcgattgtctggctgtatgc                                                                               >  1:444230‑M1/1‑85 (MQ=255)                                               aaTGACGTTACCGAGTGGACACCCGAAGAGCAGATTGATCAAAAAATTTACCGCACTAGGCGCGTATATTCGTGAAGGTAagtgcaaagataatcgattctttttcgattgtctggctgtatgcgtcaa                                                                          >  2:34609‑M1/1‑80 (MQ=255)                                                aTGACGTTACCGAGTGGACACCCGAAGAGCAGATTGATAAAAAAAAATACCGAAATAGACAAGAATAATCGAGAAGGTAagtgcaaagataatcgattctttttcgattgtctggctgtatgcgtcaaa                                                                         >  1:245844‑M1/1‑79 (MQ=255)                                                 tGACGTTACCGAGTGGCCACCCGAAGAGCAGATTGATCAAAAAATTTACCGCACTAGGCCCGTATATTCGTGAAGGTAagtgcaaagataatcgattctttttcgattgtctggctgtatgcgtcaacg                                                                        >  1:441004‑M1/1‑78 (MQ=255)                                                           gAGTGGACACCCGAAGAGCAGATTGATCAAAAAATTTACCGCACTCGGCCCGTATATTCGTGAAGGTAagtgcaaagataatcgattctttttcgattgtctggctgtatgctccaacgtgaaaccggc                                                              >  2:632560‑M1/1‑68 (MQ=255)                                                             gTGGACACCCGAAGAGCAGATTGATCAAAAAATTTACCGCACTAGGCCCGTATATTCGTGAAGGTAagtgcaaagataatcttttctttttttattgtttggttgtatgcgtcaacgtggaaccggcac                                                            <  1:500826‑M1/129‑64 (MQ=255)                                                                   agccgaAGAGCAGATTGATCAAAAAATTTACCGCACTAGGCCCGTATATTCGTGAAGGTAagtgcaaagataatcgattctttttcgattgtctggctgtatgcgtcaacgtgaaaccggcaccggaag                                                      >  2:539911‑M1/3‑60 (MQ=255)                                                                              aGATTGATCAAAAAATTTACCGCACTAGGCCCGTATATTCGTGAAGGTAagtgcaaagataatcgattctttttcgattgtctggctgtatgcgtcaacgtgaaaccggcaccggaagtgcgtgaattc                                           >  2:57072‑M1/1‑49 (MQ=255)                                                                                   gATCAAAAAATTTACCGCACTAGGCCCGTATATTCGTGAAGGTAagtgcaaagataatcgattctttttcgattgtctggctgtatgcgtcaacgtgaaaccggcaccggaagtgcgtgaattctgggg                                      >  2:445721‑M1/1‑44 (MQ=255)                                                                                   gATCAAAAAATTTACCGCACTAGGCCCGTATATTAGAGAAAAAAaaaaaaaagataatagattctttttcgattgtctggctgtatgcgtaaacgtgaaaacggcaccggaagtgcgtgaattctgggg                                      >  1:198888‑M1/1‑44 (MQ=255)                                                                                    aTCATATAATTTACCGCACGAGGCCCGTATATTCGTGAAGGTAagtgcaaagataatcgattctttttcgattgtctggctgtatgcgtcaacgtgaaaccggcaccggaagtgcttgaattctggggc                                     <  2:266112‑M1/129‑87 (MQ=255)                                                                                     tCAAAAAATTTACCGCACTAGGCCCTTATATTCGTGAAAATAagtgcaaagataatcgattctttttcgattgtctggctgtatgcgtcaacgtgaaaccggcaccggaagtgcgtgaattctggggct                                    >  1:497168‑M1/1‑42 (MQ=255)                                                                                       aaaaatTTTACCGCACTAGGCCCGTATATTCGTGAAGGTAagggcaaagataatcgattctttttcgattgtctggctgtttgtgtcaacgtgaaaccggcaccggaagtgcgtgaatgctggggctgg                                  <  1:359281‑M1/129‑90 (MQ=255)                                                                                         aaaaTTTACCGCACTAGGCCCGTATATTCGTGAAGGTAagtgcaaagataatcgattctttttcgattgtctggctgtatgcgtcaacgtgaaaccggcaccggaagtgcgtgaattctggggctggtg                                <  2:444230‑M1/129‑92 (MQ=255)                                                                                           aaTTTACCGCACTAGGCCCGTCTATTCGTGAAGGTAagtacaaaaataaacaattctttttcgattatctggctgtatgcgtcaacgtgaaaccggcaccggcagtgcgtgaattctggggctggtgga                              >  1:80527‑M1/1‑36 (MQ=255)                                                                                           aaTTTACCGCACTAGGCCCGTATATTCGTGAAGGTAaatacaaagataaacgaatctttttcgattgtctggctgtatgcgtcaacgtgaaaccggcaccggaagtgcgtgaattctggggctggtgga                              >  1:553809‑M1/1‑36 (MQ=255)                                                                                               tACCGCTCTAGGCGCGTATATTCGTGAAGGTAagtgcaaagataatcgattcttttttgattgtctggctgtatgcgtcaacgtgaaaccggcaccggaagtgcgtgaattctggggctggtggatgga                          <  2:452655‑M1/129‑98 (MQ=255)                                                                                               tACCGCACTAGGCCCGTATATTCGAGAAGGTAagtgcaaagataatcgattctttttcgattgtttggctgtatgcgtcaacgtgaaacccgcaccggaattgcgtgaattctggggctggtggctaga                          >  2:510034‑M1/1‑32 (MQ=255)                                                                                                     aCTAGGCCCGTATATTCGTGAAGGTAagtgcaaagataatcgattctttttcgattgtctggctgtatgcgtcaacgtgaaaccggcaccggaag                                                      >  2:331108‑M1/1‑26 (MQ=255)                                                                                                     aCTAGGCCCGTATATTCGTGAAGGTAagtgcaaagataatcgattctttttcgattgtctggctgtatgcgtcaacgtgaaaccggcaccggaag                                                      <  1:331108‑M1/95‑70 (MQ=255)                                                                                                     aCTAGGCCCGTATATTCGTGAAGGTAagtgcaaagataatcgattctttttcgattgtacggcattattcgtaccagtgaaaccggcaccggaagtgcgtgaactctggggccggtggatgaagctgga                    >  2:114356‑M1/1‑26 (MQ=255)                                                                                                            ccGTATATGTGTGAAGGTAagtgcaaagctaatcgattcgtttgcgattgtctggctgtatgcgtcaacgtgaaaccggcaccggaagtgcgtgaattctggggttggtgggaggagctggaagcgcag             <  2:323903‑M1/129‑111 (MQ=255)                                                                                                             cGTATATTCGTGAAGGTAagtgcaaagataatcgattctttttcgattgtctggctgtatgcgttaacgtgattccgtcatcggaagtgcgtgaaatcaggggcaggtggagggagctggaagcgcagg            <  1:93613‑M1/129‑112 (MQ=255)                                                                                                                 tatTCGTGAAGGTAagtgcaaagataatcgattctttttcgattgtctggctgtatgcgtcaacgtgaaaccggcatcggaagtgtgtgaattctggggctggtggatggagctggaagcgcaggaatc        <  1:353633‑M1/129‑116 (MQ=255)                                                                                                                  atTCGTGTAGGTAagtgcatagataatcgattctttttagattgtctggctgtatgcgtcaacgtgaaaccggcaccggaagtgcgtgaattctggggctggtggatggagctggaagcgcaggaatcc       >  1:246603‑M1/1‑13 (MQ=255)                                                                                                                       tGAAGGTAagtgcaaacatgatcgattctttttcgattgtcgggctgtatgcgtcaacgtgaaaccggcaccggaagtgcgtgaattctggggctggtggatggagctggaagcgcaggaatcccgttt  <  2:453441‑M1/129‑122 (MQ=255)                                                                                                                              |                                                                                                                          AATTTTGCCAATTTGGTAAAACAGTTGCATCACAACAGGAGATAGCAATGACGTTACCGAGTGGACACCCGAAGAGCAGATTGATCAAAAAATTTACCGCACTAGGCCCGTATATTCGTGAAGGTAGGTAATGACTCCAACTTATTGATAGTGTTTTATGTTCAGATAATGCCCGATGACTTTGTCATGCAGCTCCACCGATTTTGAGAACGACAGCGACTTCCGTCCCAGCCGTGCCAGGTGCTGC  >  NC_000913/257782‑258028

Alignment Legend
Aligned base mismatch/match (shaded by quality score): ATCG/ATCG < 3 ≤ ATCG/ATCG < 12 ≤ ATCG/ATCG < 13 ≤ ATCG/ATCG < 22 ≤ ATCG/ATCG < 41 ≤ ATCG/ATCG
Unaligned base: atcg    Masked matching base: atcg    Alignment gap: ‑    Deleted base: ‑