Predicted mutation
evidence	seq id	position	mutation	annotation	gene	description
MC JC	NC_000913	997,868	Δ6,818 bp		[elfA]–ycbF	[elfA], elfD, elfC, elfG, ycbU, ycbV, ycbF

Missing coverage evidence...
			seq id	start	end	size	←reads	reads→	gene	description
*	*	÷	NC_000913	997868	1004685	6818	37 [0]	[0] 37	[elfA]–ycbF	[elfA],elfD,elfC,elfG,ycbU,ycbV,ycbF

New junction evidence
		seq id	position	reads (cov)	reads (cov)	score	skew	freq	annotation	gene	product
*	?	NC_000913	= 997867	0 (0.000)	37 (1.230)	31/98	0.0	100%	intergenic (‑355/‑1)	ssuE/elfA	NADPH‑dependent FMN reductase/putative laminin‑binding fimbrial subunit
	?	NC_000913	1004686 =	0 (0.000)					intergenic (+29/‑82)	ycbF/pyrD	putative fimbrial chaperone YcbF/dihydroorotate dehydrogenase, type 2

AGGAGCAAAATCTGCCCTGAAACAGGTTCGGAAAACGTTTGCGTTTTTTTTGCCGCAGGTCAATTCCCTTTTGGTCCGAACTCGCACATAATA  >  NC_000913/1004638‑1004730                                                 |                                             gtcatttaaaggcattatcatatttacgaagagatcaggatgataacgtt                                             >  1:1306157‑M2/49‑50 (MQ=255) gtcatttaaaggcattatcatatttacgaagagatcaggatgataacgtt                                             >  1:1686204‑M2/49‑50 (MQ=255)  tcatttaaaggcattatcatatttacgaagagatcaggatgataacgttt                                            <  1:233686‑M2/3‑1 (MQ=255)   catttaaaggcattatcatatttacgaagagatcaggatgataacgTTTg                                           >  1:85969‑M2/47‑50 (MQ=255)     tttaaaggcattatcatatttacgaagagatcaggatgataacgTTTGcc                                         <  1:349749‑M2/6‑1 (MQ=255)      ttaaaggcattatcatatttacgaagagatcaggatgataacgTTTGCCg                                        >  1:722219‑M2/44‑50 (MQ=255)           ggcattatcatatttacgaagagatcaggatgataacgTTTGCCGCAGGt                                   >  1:666326‑M2/39‑50 (MQ=255)           ggcattatcatatttacgaagagatcaggatgataacgTTTGCCGCAGGt                                   >  1:1852785‑M2/39‑50 (MQ=255)             cattatcatatttacgaagagatcaggatgataacgTTTGCCGCAGGTCa                                 <  1:2082833‑M2/14‑1 (MQ=255)              attatcatatttacgaagagatcaggatgataacgTTTGCCGCAGGTCaa                                >  1:2222561‑M2/36‑50 (MQ=255)              attatcatatttacgaagagatcaggatgataacgTTTGCCGCAGGTCaa                                >  1:2155431‑M2/36‑50 (MQ=255)                  tcatatttacgaagagatcaggatgataacgTTTGCCGCAGGTCAATTcc                            >  1:551353‑M2/32‑50 (MQ=255)                  tcatatttacgaagagatcaggatgataacgTTTGCCGCAGGTCAATTcc                            <  1:1798079‑M2/19‑1 (MQ=255)                  tcatatttacgaagagatcaggatgataacgTTTGCCGCAGGTCAATTc                             <  1:1570710‑M2/18‑1 (MQ=255)                       tttacgaagagatcaggatgataacgTTTGCCGCAGGTCAATTCCCtttt                       >  1:1370304‑M2/27‑50 (MQ=255)                        ttacgaagagatcaggatgataacgTTTGCCGCAGGTCAATTCCCTTTTg                      >  1:210521‑M2/26‑50 (MQ=255)                         tacgaagagatcaggatgataacgTTTGCCGCAGGTCAATTCCCTTTTg                      <  1:1811317‑M2/25‑1 (MQ=255)                          acgaagagatcaggatgataacgTTTGCCGCAGGTCAATTCCCTTTTgg                     <  1:1313783‑M2/26‑1 (MQ=255)                          acgaagagatcaggatgataacgTTTGCCGCAGGTCAATTCCCTTTTGGt                    >  1:123078‑M2/24‑50 (MQ=255)                           cgaagagatcaggatgataacgTTTGCCGCAGGTCAATTCCCTTTTGGTc                   <  1:630701‑M2/28‑1 (MQ=255)                            gaagagatcaggatgataacgTTTGCCGCAGGTCAATTCCCTTTTGGTcc                  <  1:611593‑M2/29‑1 (MQ=255)                            gaagagatcaggatgataacgTTTGCCGCAGGTCAATTCCCTTTTGGTcc                  >  1:2248080‑M2/22‑50 (MQ=255)                               gagatcaggatgataacgTTTGCCGCAGGTCAATTCCCTTTTGGTCCGaa               >  1:1172605‑M2/19‑50 (MQ=255)                                agatcaggatgataacgTTTGCCGCAGGTCAATTCCCTTTTGGTCCGAAc              <  1:809818‑M2/33‑1 (MQ=255)                                 gatcaggatgataacgTTTGCCGCAGGTCAATTCCCTTTTGGTCCGAACt             <  1:16929‑M2/34‑1 (MQ=255)                                 gatcaggatgataacgTTTGCCGCAGGTCAATTCCCTTTTGGTCCGAACt             >  1:777793‑M2/17‑50 (MQ=255)                                 gatcaggatgataacgTTTGCCGCAGGTCAATTCCCTTTTGGTCCGAACt             >  1:88095‑M2/17‑50 (MQ=255)                                  atcaggatgataacgTTTGCCGCAGGTCAATTCCCTTTTGGTCCGAACTc            <  1:630214‑M2/35‑1 (MQ=255)                                    caggatgataacgTTTGCCGCAGGTCAATTCCCTTTTGGTCCGAACTCg           >  1:2194507‑M2/14‑49 (MQ=255)                                    caggatgataacgTTTGCCGCAGGTCAATTCCCTTTTGGTCCGAACTCg           >  1:944187‑M2/14‑49 (MQ=255)                                     aggatgataacgTTTGCCGCAGGTCAATTCCCTTTTGGTCCGAACTCGca         <  1:674618‑M2/38‑1 (MQ=255)                                        atgataacgTTTGCCGCAGGTCAATTCCCTTTTGGTCCGAACTCGcaca       >  1:1010609‑M2/10‑49 (MQ=255)                                        atgataacgTTTGCCGCAGGTCAATTCCCTTTTGGTCCGAACTCGcaca       >  1:992322‑M2/10‑49 (MQ=255)                                         tgataacgTTTGCCGCAGGTCAATTCCCTTTTGGTCCGAACTCGCACata     <  1:845560‑M2/42‑1 (MQ=255)                                           ataacgTTTGCCGCAGGTCAATTCCCTTTTGGTCCGAACTCGCACataat   <  1:1317369‑M2/44‑1 (MQ=255)                                           ataacgTTTGCCGCAGGTCAATTCCCTTTTGGTCCGAACTCGCACataa    <  1:1754367‑M2/43‑1 (MQ=255)                                            taacgTTTGCCGCAGGTCAATTCCCTTTTGGTCCGAACTCGCACataata  <  1:681926‑M2/45‑1 (MQ=255)                                                 |                                             AGGAGCAAAATCTGCCCTGAAACAGGTTCGGAAAACGTTTGCGTTTTTTTTGCCGCAGGTCAATTCCCTTTTGGTCCGAACTCGCACATAATA  >  NC_000913/1004638‑1004730

Alignment Legend
Aligned base mismatch/match (shaded by quality score): ATCG/ATCG < 3 ≤ ATCG/ATCG < 33 ≤ ATCG/ATCG < 34 ≤ ATCG/ATCG < 37 ≤ ATCG/ATCG < 39 ≤ ATCG/ATCG
Unaligned base: atcg    Masked matching base: atcg    Alignment gap: ‑    Deleted base: ‑