Predicted mutation
evidence	seq id	position	mutation	annotation	gene	description
MC JC	NC_000913	1,095,503	Δ10,045 bp	IS3‑mediated	ycdU–[ymdA]	ycdU, serX, ghrA, ycdX, ycdY, ycdZ, csgG, csgF, csgE, csgD, csgB, csgA, csgC, [ymdA]

Missing coverage evidence...
			seq id	start	end	size	←reads	reads→	gene	description
*	*	÷	NC_000913	1094431–1095501	1105547	10047–11117	25 [24]	[0] 81	[insF4]–[ymdA]	[insF4],insE4,ycdU,serX,ghrA,ycdX,ycdY,ycdZ,csgG,csgF,csgE,csgD,csgB,csgA,csgC,[ymdA]

New junction evidence
		seq id	position	reads (cov)	reads (cov)	score	skew	freq	annotation	gene	product
*	?	NC_000913	315229 =	NA (NA)	80 (0.840) +T	70/492	0.3	100%	noncoding (1/1255 nt)	IS3	repeat region
	?	NC_000913	1105548 =	0 (0.000)					coding (135/312 nt)	ymdA	uncharacterized protein YmdA

CGGGCGTAATAAGGTGGTTGTGAGGGATGTGGTGAATTTTTGTGAGTCACCATAAAGCGGCATTTTGATC‑CTACCCACGTAATATGGACACAGGCCTAAGCGAGGTTCTTGTTTTCAAA‑TTGTTCCGGACTGAGGCCGCCACACCAACTGTGCCGCCGCCACCGATTGTAATCACATTCGATATAATTAAACACCGTTGCCCGCATTATTTCCCGGCTGATAAAGTGTTCTCCATGGATACATTCCACTTTCAGCGAATGAAAGAAGCTTTCCACGCAGGCATTATCGTAGCAGCAACCTTTTGCGCTC  >  NC_000913/1094180‑1094488                                                                                                                                                                                                                                                             |                                                           ggggagTAATAAGGTGTTTGGGAGGGATGTGGGGAATTTGTGTGAGACACCATAAGTCGGCATTTTGTTC‑CTCCCCACGTAATATGGACACAGGCCTAAGCGAGGTTCTTGTTTTCAAA‑TTGTTCCGGACTGAGGCCGCCACACCAACTGTGCCGCCGCCACCGATTGTAATCACATTCGATATAATTAAACACCGTTGCCCGCATTATTTCCCGGCTGATAAAGTGTTCTCCATGGATACATTCCACttt                                                            <  2:281234/246‑1 (MQ=14)      ttaataaGGTGGTTGTGAGGGATGTGGTGAATTTTTGTGAGTCACCATAAAGCGGCATTTTGATC‑CTACCCACGTAATATGGACACAGGCCTAAGCGAGGTTCTTGTTTTCAAA‑TTGTTCCGGACTGAGGCCGCCACACCAACTGTGCCGCCGCCACCGATTGTAATCACATTCGATCTAATTAACCACCGTTGCCCGCATTCTTTCACGGCTGATAAAGTGTTCTCCATGGATCCATTCCACTTTCAGCg                                                       >  2:21016/2‑251 (MQ=255)      gTAATAAGGTGGTTGTGAGGGATGGGGTGAATTTTTGTGAGTCACCATAAAGCGGCATTTGGATC‑CTACCCACGTAATATGGACACAGGCCTAAGCGAGGTTCTTGTTTTCAAA‑TTGTTCCGGACTGAGGCCGCCACACCAACTGTGCCGCCGCCACCGATTGTAATCACATTCGATATAATTAAACACCGTTGCCCGCATTATTTCCCGGCTGATAAAGTGTTCTCCATGGATACATTCCACTTTCAGCg                                                       <  1:162685/251‑1 (MQ=255)            aGGTGGTTTGGAGTGATGTGGTGAATTGTTGTGAGTAAACATAATGGTGAGTTTTGAGC‑CGACCCACTCAATATGGACACAGGCCTAAGATAGGTGCT‑GTTTTTAAAGTTGCGCCGGACAGAGGCTGCCACACCAACTGTGCCGCCTCCACTGACTTTAATCACATTCGATATAATTAAACACCGTTGCCCTCATTATTTCCCGGCTGATAAAGTGTTCTCCATTGATACATTCCACTTTCAGCGAATGaa                                                 <  2:739754/251‑1 (MQ=2)            aGGTGGTTGTGAGGGATGTGGTGAATTTTTGTGAGTCACCATAAAGCGGCATTTTGATC‑CTACCCACGTAATATGGACACAGGCCTAAGCGAGGTTCTTGTTTTCAAA‑TTGTTCCGGACTGAGGCCGCCACACCAACTGTGCCGCCGCCACCGATTGTAATCACATTCGATATAATTAAACACCGTTGCCCGCATTATTTCCCGGCTGATAAAGTGTTCTCCATGGATACATTCCACTTTCAGCGAATGa                                                  >  1:20986/1‑250 (MQ=255)                ggtTGTTAGGGATGTGGTAAATTTTTGTAAGTTACCATAAAGAGGCATTTTGATC‑CTACCCACGTAATATGGACACAGGCCTAAGCGAGGTTCTTGTTTTCAAA‑TTGTTCCGGACTGAGGCCGCCACACCAACTGTGCCGCCGCCACCGATTGTAATCACATTCGATATAATTAAACACCGTTGCCCGCATTATTTCCCGGCTGATAAAGTGTTCTCCATGGATACATTCCACTTTCAGCGAATGAaagaa                                             <  1:380520/251‑1 (MQ=255)                 gtTGTGAGGGATGTGGTGAATTTTTTGGAGCCACCATAAAGCGGAATTTTGATC‑CTACCACCTTAATATGGACACAGGCATAAGCGAGGTCCTTGTTTTCAAA‑TTGTACCGGCCTGAGGCCGCCACCCCAACTGTGCCGCCGCCACCGATTGTAATCACATTCGATATAATTAAACACCGTTGCCCGCATTATTTCCCGGCTGATAAAGTGTTCTCCATGGATACATTCCACTTTCAGCGAATGAaagaag                                            <  2:744694/251‑1 (MQ=14)                       gggtaTGTGGTGATTTTTTGAGCTTCACCAAAAGGCGGCTTTTTGATCTCT‑CCCACGTAATAGGGACACAGGCCTAAGCGAGGTTTTTGTTTTAAAA‑TTGTTCCGGTCGGAGGCCGCCACTCCAACTGTGCCGCCGCCACCGATTGTAATCACATTCGATATAATTAAACACCGTTGCCCGCATTATTTCCCGGCTGATAAAGTGTTTTCCATGGATACATTCCACTTTCAGCGAATGAAAGAAGCTTTcc                                      <  2:135601/247‑1 (MQ=11)                       gggactgtgGTGCATTGTTGTGAGTCACCAGAACGCGGCACTCTGATC‑CTACCCACGTAATATGGACACAGGTTTACGGGAGGTTCTTTTTTTCAAA‑TTGTTCCGGCCTGAGGCCGCCACACCAACTGTGCCGCCGCCACCGATTGTAATCACATTCGATATAATTAAACACCGTTGCCCGCATTATTCCCCGGCTGATAAAGTGTTCTCCATGGATACATTCCACTTTCAGCGAATGAAAGAAGCTTTcc                                      <  1:524889/246‑1 (MQ=11)                        gggATGTGGTGAATTTTTGTGAGTCACCATAAAGCGGCATTTTGATC‑CTACCCACGTAATATGGACACAGGCCTAAGCGAGGTTCTTGTTTTCAAA‑TTGTTCCGGACTGAGGCCGCCACACCACCTGTGCCGCCGCCACCGCTTGTAATCACATTCGATATAATTAAACACCGTTGCCCGCATTATTTCCCGGCTGATAAAGTGTTCTCCATGGATACATTCCACTTTCAGCGAATGAAAGAAGCTTTcc                                      >  2:691364/1‑250 (MQ=255)                                 tgAATTTTTGTGAGTCACCATAAAGCGGCATTTTGATC‑CTACCCACGTAATATGGACACAGGCCTAAGCGAGGTTCTTGTTTTCAAA‑TTGTTCCGGACTGAGGCCGCCACACCAACTGTGCCGCCGCCACCGATTGTAATCACATTCGATATAATTAAACACCGTTGCCCGCATTATTTCCCGGCTGATAAAGTGTTCTCCATGGATACATTCCACTTTCAGCGAATGAAAGAAGCTTTCCACGCAGGCAt                            >  1:736942/1‑251 (MQ=255)                                      ttttGTGAGTCACCATAAAGCGGCCTTTTGATC‑CTACCCACGTAATATGGACACAGGCCTAAGCGAGGTTCTTGTTTTCAAA‑TTGTTCCGGACTGAGGCCGCCACACCAACTGTGCCGCCGCCACCGATTGTAATCACATTCGATATAATTAAACACCGTTGCCCGCATTATTTCCCGGCTGATAAAGTGTTCTCCATGGATACATTCCACTTTCAGCGAATGAAAGAAGCTTTCCACGCAGGCATTATCg                       >  1:963639/1‑251 (MQ=255)                                         tgtgAGTCACCATAAAGCGGCATTTTGATC‑CTACCCACGTAATATGGACACAGGCCTAAGCGAGGTTCTTGTTTTCAAA‑TTGTTCCGGACTGAGGCCGCCACACCAACTGTGCCGCCGCCACCGATTGTAATCACATTCGATATAATTAAACACCGTTGCCCGCATTATTTCCCGGCTGATAAAGTGTTCTCCATGGATACATTCCACTTTCAGCGAATGAAAGAAGCTTTCCACGCAGGCATTATCGTat                    >  1:67890/1‑250 (MQ=40)                                          gtgAGTAACCATAAAGCGGCATTTTGATC‑CTACCCACGTAATATGGACACAGGCCTAAGCGAGGTTCTTGTTTTCAAA‑TTGTTCCGGACTGAGGCCGCCACACCAACTGTGCCGCCGCCACCGATTGTAATCACATTCGATATAATTAAACACCGTTGCCCGCATTATTTCCCGGCTGATAAAGTGTTCTCCATGGATACATTCCACTTTCAGCGAATGAAAGAAGCTTTCCACGCAGGCATTATCGTag                    <  1:432395/250‑1 (MQ=38)                                              gTCACCATAAAGCGGCATTTTGATC‑CTACCCACGTAATATGGACACAGGCCTAAGCGAGGTTCTTGTTTTCAAA‑TTGTTCCGGACTGAGGCCGCCACACCAACTGTGCCGCCGCCACCGATTGTAATCACATTCGATATAATTAAACACCGTTGCCCGCATTATTTCCCGGCTGATAAAGTGTTCTCCATGGATACATTCCACTTTCAGCGAATGAAAGAAGCTTTCCACGCAGGCATTATCGTAgcagca               <  1:410375/251‑1 (MQ=38)                                               tCACCTTAAAGCGTCATTTTGATC‑CTACCCACGTAATATGGACACAGGCCTAAGCGAGTTTCTTGTTTTCAAA‑GTGTTCCGGCCTGAGGCCGCCACACCAACTGTGCCGCCGCCACCGATTGTAATCACATTCGATATAATTAAACACCGTTGCCCGCATTATTTCCCGGCTGATAAAGTGTTCTCCATGGATACATTCCACTTTCAGCGAATGAAAGAAGCTTTCCACGCAGGCATTATCGTAgcagca               <  1:793834/250‑1 (MQ=255)                                                 aCCATAAAGCGGCATTTTGATC‑CTACCCACGTAATATGGACACAGGCCTAAGCGAGGTTCTTGTTTTCAAA‑TTGTTCCGGACTGAGGCCGCCACACCAACTGTGCCGCCGCCACCGATTGTAATCACATTCGATATAATTAAACACCGTTGCCCGCATTATTTCCCGGCTGATAAAGTGTTCTCCATGGATACATTCCACTTTCAGCGAATGAAAGAAGCTTTcc                                      >  1:66587/1‑225 (MQ=38)                                                 aCCATAAAGCGGCATTTTGATC‑CTACCCACGTAATATGGACACAGGCCTAAGCGAGGTTCTTGTTTTCAAA‑TTGTTCAGGACTGAGGCCGCCACACCAACTGTGCCGCCGCCACCGATTGTAATCACATTCGATATAATTAAACACCGTTGCCCGCATTATTTCCCGGCTGATAAAGTGTTCTCCATGGATACATTCCACTTTCAGCGAATGAAAGAAGCTTTCCACGCAGGCATTATCGTAGCAGCAAcc            >  1:50288/1‑251 (MQ=37)                                                 aCCATAAAGCGGCATTTGGATC‑CTACCCCCGTAATAGGGACACAGGCCTAAGCGAGGTTCTTGTTTTAAAA‑TGGTTCCGGACTGAGGCCGCCACACCAACTGTGCCGCCGCCACCGATTGTAATCACATTCGATATAATTAAACACCGTTGCCCGCATTATTTCCCGGCTGATAAAGTGTTCTCCATGGATACATTCCACTTTCAGCGAATGAAAGAAGCTTTcc                                      <  2:66587/225‑1 (MQ=255)                                                       aaGCGGCATTTTGATC‑CTACCCACGTAATATGGACACAGGCCTAAGCGAGGTTCTTGTTTTCAAA‑TTGTTCCGGACTGAGGCCGCCACACCAACTGTGCCGCCGCCACCGATTGTAATCACATTCGATATAATTAAACACCGTTGCCCGCATTATTTCCCGGCTGATAAAGTGTTCTCCATGGATACATTCCACTTTCAGCGAATGAAAGAAGCTTTCCACGCAGGCATTATCGTAGCAGCAACCTTTTgc      >  1:489966/1‑251 (MQ=33)                                                        aGCGGCATTTTGATC‑CTACCCACGTAATATGGACACAGGCCTAAGCGAGGTTCTTGTTTTCAAA‑TTGTTCCGGACTGAGGCCGCCACACCAACTGTGCCGCCGCCACCGATTGTAATCACATTCGATATAATTAAACACCGTTGCCCGCATTATTTCCCGGCTGATAAAGTGTTCTCAATGGATACATTCCACTTTCAGCGAATGAACGAAGCTTTCCACGCAGGCATTATCGTACCAGCACCCtttttcg     >  2:333249/1‑248 (MQ=255)                                                         gCGGCATTTTGATC‑CTACCCACGTAATATGGACACAGGCCTAAGCGCGGTTCTTGTTTTCAAA‑TTGTTCCGGCCTGAGGCCGCCACACCACCTGTGCCGCCACCACCGATTGTAATCACATTCGCTATAATTAAACACCGTTGCCCGCCTTATTTCCCGGCTGATAAAGTGTTCTCCATGGATACATTCCACTTTCAGCGAATGAAAGAAGCTTTCCTCGCAGGCATTATCGTAGCAGCAACCTTTTgcgc    >  1:45977/1‑251 (MQ=11)                                                          cGGCATTTTGATC‑CTACCCACGTAATATGGACACAGGCCTAAGCGCGGTTCTTGTTTTCAAA‑TTGTTCCGGACTGAGGCCGCCACACCAACTGTGCCGCCGCCACCGATTGTAATCACATTCGATATAATTAAACACCGTTGCCCGCATTATTTCCCGGCTGATAAAGTGTTCTCCATGGATACATTCCACTTTCAGCGAATGAAAGAAGCTTTCCACGCAGGCATTATCGTAGCAGCAACCTTTTGCGCt   >  2:975211/1‑251 (MQ=17)                                                           ggCATTTTGATC‑CTACCCACGTAATATGGACACAGGCCTAAGCGAGGTTCTTGTTTTCAAA‑TTGTTCCGGACTGAGGCCGCCACACCAACTGTGCCGCCGCCACCGATTGTACTCACATTCGATATAATTAAACACCGTTGCCCGCATTATTTCCCGGCTGATAAAGTGTTCTCCATGGATACATTCCCCTTTCAGCGAATGAAAGAAGCTTTCCACGCAGGCATTATCGTAGCAGCAACCTTTTTCGCTc  >  1:652958/1‑251 (MQ=17)                                                           ggCATTTTGATC‑CTACCCACGTAATATGGACACAGGCCTAAGCGAGGTTCTTGTTTTCAAA‑TTGTTCCGGACTGAGGCCGCCACACCAACTGTGCCGCCGCCACCGATTGTAATCACATTCGATATAATTAAACACCGTTGCCCGCATTATTTCCCGGCTGATAAAGTGTTCTCCATGGATACATTCCACTTTCAGCGAATGAAAGAAGCTTTCCACGCAGGCATTATCGTAGCAGCAACCTTTTGCGCTc  >  1:515516/1‑251 (MQ=32)                                                                                                                                                                                                                                                             |                                                           CGGGCGTAATAAGGTGGTTGTGAGGGATGTGGTGAATTTTTGTGAGTCACCATAAAGCGGCATTTTGATC‑CTACCCACGTAATATGGACACAGGCCTAAGCGAGGTTCTTGTTTTCAAA‑TTGTTCCGGACTGAGGCCGCCACACCAACTGTGCCGCCGCCACCGATTGTAATCACATTCGATATAATTAAACACCGTTGCCCGCATTATTTCCCGGCTGATAAAGTGTTCTCCATGGATACATTCCACTTTCAGCGAATGAAAGAAGCTTTCCACGCAGGCATTATCGTAGCAGCAACCTTTTGCGCTC  >  NC_000913/1094180‑1094488

Alignment Legend
Aligned base mismatch/match (shaded by quality score): ATCG/ATCG < 3 ≤ ATCG/ATCG < 13 ≤ ATCG/ATCG < 14 ≤ ATCG/ATCG < 32 ≤ ATCG/ATCG < 39 ≤ ATCG/ATCG
Unaligned base: atcg    Masked matching base: atcg    Alignment gap: ‑    Deleted base: ‑