Predicted mutation
evidence	seq id	position	mutation	annotation	gene	description
MC JC	NC_000913	2,023,805	(CTTTA)2→1	intergenic (+127/‑159)	fliR → / → rcsA	flagellar export pore protein/transcriptional regulator of colanic acid capsular biosynthesis

Missing coverage evidence...
			seq id	start	end	size	←reads	reads→	gene	description
*	*	÷	NC_000913	2023796	2023800	5	51 [0]	[0] 53	fliR/rcsA	flagellar export pore protein/transcriptional regulator of colanic acid capsular biosynthesis

New junction evidence
		seq id	position	reads (cov)	reads (cov)	score	skew	freq	annotation	gene	product
*	?	NC_000913	2023801 =	0 (0.000)	47 (1.230)	38/266	0.1	100%	intergenic (+123/‑167)	fliR/rcsA	flagellar export pore protein/transcriptional regulator of colanic acid capsular biosynthesis
	?	NC_000913	= 2023795	0 (0.000)					intergenic (+117/‑173)	fliR/rcsA	flagellar export pore protein/transcriptional regulator of colanic acid capsular biosynthesis

GAATTGCCATTAATATAATTCCGTAACGTTTATCATGTTATCCTAAGGATTATCCGAAAAATAATACCTACGAACATCTTCCAGGATACTCCTGCAGCGAAATATTTGTTTTAAGCTCACTCACATATCGCAACATTTACTTTACTTTAAGACAATTCCAGGCAAATTATACAACACTTTACGGGATAGTAAGTCCGCCTGAAAAATCGCGAGAGTGGCGCATTAGGTGACCCATGTTGTTCCGTTTAGTCATGATGAAATATTCAGGTAAGGGGAATTATCG  >  NC_000913/2023661‑2023943                                                                                                                                             |                                                                                                                                               ttagtgaattgccattaatataattccgtaacgtttatcatgttatcctaaggattatccgaaaaataatacctacgaacatcttccaggatactcctgcagcgaaatatttgttttaagctcactcccctatcgcgacattt                                                                                                                                              <  2:324031‑M1/3‑1 (MQ=255)    gtgaattgccattaatataattccgtaacgtttatcatgttatcctaaggattatccgaaaaataatacctacgaacatcttccaggatactcctgcagcgaaatatttgttttaagctcacttacatatcgcaacaTTTACt                                                                                                                                           <  2:253214‑M1/6‑1 (MQ=255)     tgaattgccattaatataattccgtaacgtttatcatgttatcctaaggattatccgaaaaataatacctacgaacatcttccaggatgctcctgcatcgaaatatttgttttacgctcactcacatatcgcaaaaTTTGCtt                                                                                                                                          <  2:273532‑M1/7‑1 (MQ=255)     taaattgacattcatataattccgtaacgtttatcatgttatcctaaggattatccgaaaaataatacctacgaacatcttccaggatactcctgcagcgaaatatttgttttaagctcactcacatatcgcaacaTTTACtt                                                                                                                                          >  1:678298‑M1/137‑143 (MQ=255)        attgtcattattatcatgctataaggtttatctggttatcctaaggattatccgaaaaataatacctacgaacatcttccaggatactcctgcagcgaaatagttgttttaagctcactcacatatcgcaacaTTTACTTTaa                                                                                                                                       >  1:614359‑M1/134‑143 (MQ=255)        attgccattaatataattccgtaacgtttatcatgttatcctaaggattatccgaaaaataatacctacgaacatcttccaggatactcctgcagcgaaatatttgttttaagctcactcacatatcgcaacaTTTACTTTaa                                                                                                                                       >  2:117750‑M1/134‑143 (MQ=255)          tgtcattaatataattccgtaacgtttatcatgttatcctaaggattatccgaaaaataatacctacgaacatcttccaggatactcctgcagcgaaatatttgttttaagctcactcacatatcgcaacaTTTACTTTAAGa                                                                                                                                     >  1:276083‑M1/132‑143 (MQ=255)            ccattaatataattccgtaacgtttatcatgttatcctaaggattatccgaaaaataatacctacgaacatcttccaggatactcctgtggcgaaaaatttattttaagctcactcacatatcgcaacaTTTACTTTAAGACa                                                                                                                                   <  2:520830‑M1/14‑1 (MQ=255)                    ataattccgtaacgtttatcatgttatcctaaggattatccgaaaaataatacctacgaacatcttccaggatactcctgccgcggtatctttcactcaagctcactcacatatcgcaacaTTTACTTTAAGACAATTCCAgg                                                                                                                           <  2:521000‑M1/22‑1 (MQ=255)                           cgtaacgtttatcatgttatcctaaggattatccgaaaaataatacctacgaacatcttccaggatactcctgcagcgaaatatttgttttaagctcactcacatatcgcaacaTTTACTTTAAGACAATTCCAGGCAAATta                                                                                                                    <  2:476448‑M1/29‑1 (MQ=255)                           cgtaacgtttaccatgttatcctaaggattatccgaaaaataatacctacgaacatcttccaggatactcctgcagcgaaatatttgttttaagctcactcacatatcgcaacaTTTACTTTAAGACAATTCCAGGCAAATta                                                                                                                    >  1:213929‑M1/115‑143 (MQ=255)                             taacgtttatcatgttatcctaaggattatccgaaaaataatacctacgaacatcttccaggatactcctgcagcgaaatatttgttttaagctcactcacatatcgcaacaTTTACTTTAAGACAATTCCAGGCAAATtata                                                                                                                  >  2:459031‑M1/113‑143 (MQ=255)                               acgtttatcatgttatcctaaggattatccgaaaaataatacctacgaacatcttccaggatactcctgcagcgaaatatttgttttaagctcactcacatatcgcaacaTTTACTTTAAGACAATTCCAGGCAAATTATaca                                                                                                                <  2:548187‑M1/33‑1 (MQ=255)                                   ttatcgtgttatcctaaggattatccgaaaaataatacctacgaacatcttccaggatactcctgcagcgaaatatttgttttaagctcactcacatctcgcaacaTTAACTTTAAGACAATTCCAGGCAAATaatacaaaac                                                                                                            <  1:129031‑M1/37‑4 (MQ=255)                                       catgtaatcctaaggattatccgaaaaataatacctacgaacatcttccaggatactcctgcagcgaaatctttgttttaagctcactcacatatcgcaacaTTTACTTTAAGACAATTCCAGGCAAATTATACAACACTTTa                                                                                                        <  1:595158‑M1/41‑1 (MQ=255)                                        atgttatcctaaggattatccgaaaaataatacctacgaacatcttccaggatactcctgcagcgaaatatttgttttaagctcactcacatatcgcaacaTTTACTTTAAGACAATTCCAGGCAAATTATACAACACTTTAc                                                                                                       <  1:34623‑M1/42‑1 (MQ=255)                                         tgttatcctaaggattatccgaaaaataatacctacgaacatcttccaggatactcctgcagcgaaatatttgttttaagctcactcacatatcgcaacaTTTACTTTAAGACAATTCCAGGCAAATTATACAACACTTTACg                                                                                                      >  2:234923‑M1/101‑143 (MQ=255)                                          gttatcctaaggattatccgaaaaataatacctacgaacatcttccaggatactcctgcagcgaaatatttgttttaagctcactcacatatcgcaacaTTTACTTTAAGACAATTCCAGGCAAATTATACAACACTTTACgg                                                                                                     >  2:616993‑M1/100‑143 (MQ=255)                                                ctaaggattatccgaaaaataatacctacgaacatcttccaggatactcctgcagcgaaatatttgttttaagctcactcacatatcgcaacaTTTACTTTAAGACACTGCGAGGCAGAGTATACAACACTTTACGGGATAGt                                                                                               <  2:297565‑M1/50‑1 (MQ=255)                                                 taaggattatccgaaaaataatacctacgaacatcttccaggatactcctgcagcgaaatatttgttttaagctcactcacatatcgcaacaTTTCCTTTAAGACAATTCCCGGCCAATTATACATCCCTTTCCCGTATAgtt                                                                                              <  2:189522‑M1/51‑2 (MQ=255)                                                  aaggattatccgaaaaataatacctacgaacatcttccaggatactcctgcagcgaaatatttgttttaagctcactcacatatcgcaacaTTTACTTTAAGACAATTCCAGGCAAATTATACAACACTTTACGGGATAGTaa                                                                                             <  2:51257‑M1/52‑1 (MQ=255)                                                       ttatccgaaaaataatacctacgaacatcttccaggatactcctgcagcgaaatatttgttttaagctcactcacatataatacccACTACATTAAGACAATTCCAGGCAAATTATACAACACTTTACGGGATAGTAAGTCCg                                                                                        <  2:330259‑M1/57‑1 (MQ=255)                                                            cgaaaaataatacctacgaacatcttccaggatactcctgcagcgaaatatttgttttaagctcacacacatatcgcaacaTTTACTTTAAGACACATCCAGGCAAATTATACAACACTTTACGGGATAGTAAGACCGCATGa                                                                                   <  1:35689‑M1/62‑1 (MQ=255)                                                             gaaaaataatacctacgaacatcttccaggatactcctgcagcgaaatatttgttttaagctcactcacatatcgcaacaTTTACTTTAAGACAATTCCAGGCAAATTATACAACACTTTACGGGCTAGTACGTCCGCCTgac                                                                                  <  2:252464‑M1/63‑2 (MQ=255)                                                              aaaaattatacctacgaacatcttccaggatactcctgcagcgaaatatttgttttaagctcactcacatatcgcaacaTTTACTTTAAGACAATTCCAGGCAAATTATACAACACTTTACGGGATAGTAAGTCCGCCTGaaa                                                                                 >  1:298001‑M1/80‑143 (MQ=255)                                                              aaaaataatacctacgaacatcttccaggatactcctgcagcgaaatatttgttttaagctcactcacatatcgcaacaTTTACTTTAAGACAATTCCAGGCAAATTATACAACACTTTACGGGATAGTAAGTCCGCCTGaaa                                                                                 >  1:240576‑M1/80‑143 (MQ=255)                                                              aaaaataatacctacgaacatcttccaggatactcctgcagcgaaatatttgttttaagctcactcacatatcgcaacaTTTACTTTAAGACAATTACAGGCAAATTATACAACACTTTACGAGATAGTGAGTCCGCATGaaa                                                                                 <  1:426368‑M1/64‑1 (MQ=255)                                                                      tacctacgaacatcttccatgcttctcctgcagcgaaatatttgttttaagctcactcacatatcgcaacaTTTACTTTAAGACAATTCCAGGCAAATTATACAACACTTTACGGGATAGTAAGTCCGCCTGAAAAATCGCga                                                                         >  1:41374‑M1/72‑143 (MQ=255)                                                                      tacctacgaacatcttccacgatactcctgcagcgaaatatttgttttaagttgactcacatatcgcaacaTTTACTTTAAGACAATTCCAGGCAAATTATACAACACTTTACGGGATAGTAAGTCCGCCTGAAAAATCGCga                                                                         >  2:406574‑M1/72‑143 (MQ=255)                                                                      tacctaccaacatcttccagtatacttctgcagcgaaatatttgttttaagctcactcacatatcgcaacaTTTACTTTAAGACAATTCCAGGCAAATTATACAACACTTTACGGGATAGTAAGTCCGCCTGAAAAATCGCga                                                                         >  1:8610‑M1/72‑143 (MQ=255)                                                                      gacctacgaacatcttccaggatactcctgcagcgaaatatttgttttaagctcactcacatatcgcaacaTTTACTTTAAGACAATTCCAGGCAAATTATACAACACTTTACGGGATAGTAAGTCCGCCTGAAAAATCGCga                                                                         >  1:68553‑M1/72‑143 (MQ=255)                                                                          tacgaacatcttccaggatactcctgcagcgaaatatttgttttaagctcactcacatatcgcaacaTTTACTTTAAGACAATTCCAGGCAAATTATACAACACTTTACGGGATAGTAAGTCCGCCAGAAAAAACGCGAGAGt                                                                     <  1:629482‑M1/76‑1 (MQ=255)                                                                             gaacatcttccaggatactcctgcagcgaaatatttgttttaagctcactcacatatcgcaacaTTTACTTTAAGACAATTCCAGGCAAATTATACAACACTTTACGGGATAGTAAGTCCGCCTGAAAAATCGCGAGAGTGgc                                                                  >  1:188143‑M1/65‑143 (MQ=255)                                                                              aacatcttccaggatactcctgcagcgaaatctttgttttaagctcactcacatatcgcaacaTTTAGTTTACGACAATTCCAGGCAAATTATACAACACTTTCCGGGGTAGTAAGGCCGCCTGAAGAAacgcgagagggggg                                                                 <  2:302571‑M1/80‑6 (MQ=255)                                                                              aacatcttccaggatactcctgcagcgaaatatttgttttaagctcactcacatatcgcaacaTTGCATTTAAGACAGTTCCAGGCAAATTATACAACACTTTAGGGGGTAGTAAGTCAGCTTGTAGAATGGCGAGAGTGgcg                                                                 <  2:301936‑M1/80‑1 (MQ=255)                                                                                  tcggccacgctactcctgctgccaaatatttgtcttgagctcactcacatatcgcaacaTTTACTTTAGTACATTTCCAGGCAAACTATACAAGCCTTTACGGGATAGTAAGTCCGCCTGAAAAATCGCGAGAGTGGCGCAtt                                                             >  1:647487‑M1/60‑143 (MQ=255)                                                                                         ggatactcctgcagcgaaatatttgttttaagctcactcacatatcgcaacaTTTACTTTAAGACAATTCCAGGCAAATTATACAACACTTTACGGGATAGTAAGTCCGCCTGAAAAATCGCGAGAGTGGCGCATTAGGTGAc                                                      >  2:218845‑M1/53‑143 (MQ=255)                                                                                                 ctgcagcgaaatatttgttttaagctcactcacatatcgcaacaTTTACTTTAAGACAATTCCAGGCAAATTATACACCACTTTACGGGATAGTACGTCCGCCTGAAAAATCGCGAGCGTGGCGCATTAGGCGACCCAggttg                                              <  1:212673‑M1/99‑1 (MQ=255)                                                                                                       cgaaatatttgttttaagctcacccgcatatcgcaacaTTTACTTTACGACAATTCCAGGCCAATTATACAACACTTTACTGGATAGTAAGTCCGCCTGAAAAATCGCGAGAGTGGCGCATTAGGTGACCCATGTTGTTCCGt                                        >  1:368211‑M1/39‑143 (MQ=255)                                                                                                        gaaataattgatttaagctcactcacatatcgcaacaTTTACTGTAAGACAATTCCAGGCAAATTATACAACAATTTACGGGATAGTAAGTCCGCCTGAAAAATCGCGAGAATGGCGCATTAGGTGACCCATGTTGTTCCGtt                                       >  2:47168‑M1/38‑143 (MQ=255)                                                                                                          aatatttgttttaagttcactcacatatcgcaacaTTTACTTTAAGACAATTCCAGGCAAATTATACAACTCTTTACGGGATAGTAAGTCCGCCTGAAAAATCGCGAGAGTGGCGCATTAGGTGACCCATGTTGTTCCGTTTa                                     >  1:25052‑M1/36‑143 (MQ=255)                                                                                                              tttgttttaagctcactcacatatcgcaacaTTTACTTTAAGACAATTCCAGGCAAATTATACAACACTTTACGGGATAGTAAGTCCGCCTGAAAAATCGCGAGAGTGGCGCATTAGGTGACCCATGTTGTTCCGTTTAGTCa                                 <  1:116756‑M1/112‑1 (MQ=255)                                                                                                                  ttttaagctcactcacatatcgcaacaTTTACTTTAAGACAATTCCAGGCAAATTATACAACACTTTACGGGATAGTAAGTCCGCCTGAAAAATCGCGAGAGTGGCGCATTAGGTGACCCATGTTGTTCCGTTTAGTCatgat                             <  2:520258‑M1/116‑1 (MQ=255)                                                                                                                    ttaagctcactcacatatcgcaacaTTTACTTTAAGACAATTCCAGGCAAATTATACAACACTTTACGGGATAGTAAGTCCGCCTGAAAAATCGCGAGAGTGGCGCATTAGGTGACCCATGTTGTTCCGCCTAGTtattatgg                           <  2:59220‑M1/118‑2 (MQ=255)                                                                                                                             ctcacatatcgcaacaTTTACTTTAAGACAATTCCAGGCAAATTATACAACACTTTACGGGATAGTAAGTCCGCCTGAAAAATCGCGAGAGTGGCGCATTAGGTGACCCATGTTGTTCCGTTTAGTCATGATGAAATATTCAg                  >  2:43477‑M1/17‑143 (MQ=255)                                                                                                                             ctcacatatcgcaacaTTTACTTTAAGACAATTCCAGGCAAATTATACAACACTTTACGGGATAGTAAGTCCGCCTGAAAAATCGCGAGAGTGGCGCATTAGGTGACCCATGTTGTTCCGTTTAGTCATGATGAAATATTCAg                  >  1:189522‑M1/17‑143 (MQ=255)                                                                                                                              tcacatatcgcaacaTTTACTTTAAGACAATTCCAGGCAAATTATACAACACTTTACGGGATAGTAAGTCCGCCTGAAAAATCGCGAGAGTGGCGCATTAGGTGACCCATGTTGTTCCGTTTAGTCATGATGAAGTATGCAgg                 <  1:679722‑M1/128‑1 (MQ=255)                                                                                                                                  atatcgcaacaTTTACTTTAAGACAATTCCAGGCAAATTATACAACACTTTACGGGATAGTAAGTCCGCCTGAAAAATCGCGAGAGTGGCGCATTAGGTGACCCATGTTGTTCCGTTTAGTCATGATGAAATATTCAGGTAAg             <  1:318621‑M1/132‑1 (MQ=255)                                                                                                                                      cgcaacaTTTACTTTAAGACAATTCCAGGCAAATTATACAACACTTTACGGGATAGTAAGTCCGCCTGAAAAATCGCGAGAGTGGCGCATTAGGTGACCCATGGTGTTACGACGAGCCCAGATGAACTAGACAGCTAAGGGGa         <  1:657010‑M1/136‑1 (MQ=255)                                                                                                                                      cgcaacaCTTACTTTAAGACAATTCCAGGCAAATTATACAACACTTTACGGGATAGTAAGTCCGCCTGAAAAATCGCGAGAGTGGCGCATTAGGTGACCCATGTTGTTCCGTTTAGTCATGATGAAATATTCAGGTAAGGGGa         >  2:291974‑M1/8‑143 (MQ=255)                                                                                                                                            aTTTACTTTAAGACAATTCCAGGCAAATTATACAACACTTTACGGGATAGTAAGTCCGCCTGAAAAATCGCGAGAGTGGCGCATTAGGTGACCCATGTTGTTCCGTTTAGTCATGATGAAATATTCAGGTAAGGGGAATTATc   >  2:34623‑M1/2‑143 (MQ=255)                                                                                                                                             TTTACTTTAAGACAATTCCAGGCAAATTATACAACACTTTATGGGTTAGTAAGTCCGCCTGAAAAATCGCGAGAGTGGCGCCTTAGGTGACCCATGTTGTTCCGTTTAGTCATGATGCAATCTTCAGATCAGGGGAATTATCg  <  1:320081‑M1/143‑1 (MQ=255)                                                                                                                                             TTTACTTTAAGACAATTCCAGGCAAATTATACAACACTTTACGGGATAGTAAGTCCGCCTGAAAAATCGCGAGAGTGGCGCATTAGGTGACCCATGTTGTTCCGTTTAGTCATGATGGAATATTCAGGTAAGGGGCATTATCg  <  2:526210‑M1/143‑1 (MQ=255)                                                                                                                                             |                                                                                                                                               GAATTGCCATTAATATAATTCCGTAACGTTTATCATGTTATCCTAAGGATTATCCGAAAAATAATACCTACGAACATCTTCCAGGATACTCCTGCAGCGAAATATTTGTTTTAAGCTCACTCACATATCGCAACATTTACTTTACTTTAAGACAATTCCAGGCAAATTATACAACACTTTACGGGATAGTAAGTCCGCCTGAAAAATCGCGAGAGTGGCGCATTAGGTGACCCATGTTGTTCCGTTTAGTCATGATGAAATATTCAGGTAAGGGGAATTATCG  >  NC_000913/2023661‑2023943

Alignment Legend
Aligned base mismatch/match (shaded by quality score): ATCG/ATCG < 3 ≤ ATCG/ATCG < 12 ≤ ATCG/ATCG < 13 ≤ ATCG/ATCG < 27 ≤ ATCG/ATCG < 41 ≤ ATCG/ATCG
Unaligned base: atcg    Masked matching base: atcg    Alignment gap: ‑    Deleted base: ‑