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

TTAGTGAATTGCCATTAATATAATTCCGTAACGTTTATCATGTTATCCTAAGGATTATCCGAAAAATAATACCTACGAACATCTTCCAGGATACTCCTGCAGCGAAATATTTGTTTTAAGCTCACTCACATATCGCAACATTTACTTTACTTTAAGACAATTCCAGGCAAATTATACAACACTTTACGGGATAGTAAGTCCGCCTGAAAAATCGCGAGAGTGGCGCATTAGGTGACCCATGTTGTTCCGTTTAGTCATGATGAAATATTCAGGTAAGGGGAA  >  NC_000913/2023656‑2023937                                                                                                                                            |                                                                                                                                               ttaGTGAATTGCCATTAATATAATTCCGTAACGTTTATCATGTTATCCTAAGGATTATCCGAAAAATAATACCTACGAACATCTTCCAGGATACTCCTGCAGCGAAATATTTGTTTTAAGCTCACTCCCCTATCGCGACAttt                                                                                                                                             <  2:324031‑M2/143‑4 (MQ=255)    gTGAATTGCCATTAATATAATTCCGTAACGTTTATCATGTTATCCTAAGGATTATCCGAAAAATAATACCTACGAACATCTTCCAGGATACTCCTGCAGCGAAATATTTGTTTTAAGCTCACTTACATATCGCAACAtttact                                                                                                                                          <  2:253214‑M2/143‑7 (MQ=255)     taaattGACATTCATATAATTCCGTAACGTTTATCATGTTATCCTAAGGATTATCCGAAAAATAATACCTACGAACATCTTCCAGGATACTCCTGCAGCGAAATATTTGTTTTAAGCTCACTCACATATCGCAACAtttactt                                                                                                                                         >  1:678298‑M2/3‑136 (MQ=255)     tGAATTGCCATTAATATAATTCCGTAACGTTTATCATGTTATCCTAAGGATTATCCGAAAAATAATACCTACGAACATCTTCCAGGATGCTCCTGCATCGAAATATTTGTTTTACGCTCACTCACATATCGCAAAAtttgctt                                                                                                                                         <  2:273532‑M2/143‑8 (MQ=255)        aTTGTCATTATTATCATGCTATAAGGTTTATCTGGTTATCCTAAGGATTATCCGAAAAATAATACCTACGAACATCTTCCAGGATACTCCTGCAGCGAAATAGTTGTTTTAAGCTCACTCACATATCGCAACAtttactttaa                                                                                                                                      >  1:614359‑M2/1‑133 (MQ=255)        aTTGCCATTAATATAATTCCGTAACGTTTATCATGTTATCCTAAGGATTATCCGAAAAATAATACCTACGAACATCTTCCAGGATACTCCTGCAGCGAAATATTTGTTTTAAGCTCACTCACATATCGCAACAtttactttaa                                                                                                                                      >  2:117750‑M2/1‑133 (MQ=255)          tGTCATTAATATAATTCCGTAACGTTTATCATGTTATCCTAAGGATTATCCGAAAAATAATACCTACGAACATCTTCCAGGATACTCCTGCAGCGAAATATTTGTTTTAAGCTCACTCACATATCGCAACAtttactttaaga                                                                                                                                    >  1:276083‑M2/1‑131 (MQ=255)            ccATTAATATAATTCCGTAACGTTTATCATGTTATCCTAAGGATTATCCGAAAAATAATACCTACGAACATCTTCCAGGATACTCCTGTGGCGAAAAATTTATTTTAAGCTCACTCACATATCGCAACAtttactttaagaca                                                                                                                                  <  2:520830‑M2/143‑15 (MQ=255)                    ataATTCCGTAACGTTTATCATGTTATCCTAAGGATTATCCGAAAAATAATACCTACGAACATCTTCCAGGATACTCCTGCCGCGGTATCTTTCACTCAAGCTCACTCACATATCGCAACAtttactttaagacaattccagg                                                                                                                          <  2:521000‑M2/143‑23 (MQ=255)                           cGTAACGTTTATCATGTTATCCTAAGGATTATCCGAAAAATAATACCTACGAACATCTTCCAGGATACTCCTGCAGCGAAATATTTGTTTTAAGCTCACTCACATATCGCAACAtttactttaagacaattccaggcaaatta                                                                                                                   <  2:476448‑M2/143‑30 (MQ=255)                           cGTAACGTTTACCATGTTATCCTAAGGATTATCCGAAAAATAATACCTACGAACATCTTCCAGGATACTCCTGCAGCGAAATATTTGTTTTAAGCTCACTCACATATCGCAACAtttactttaagacaattccaggcaaatta                                                                                                                   >  1:213929‑M2/1‑114 (MQ=255)                             tAACGTTTATCATGTTATCCTAAGGATTATCCGAAAAATAATACCTACGAACATCTTCCAGGATACTCCTGCAGCGAAATATTTGTTTTAAGCTCACTCACATATCGCAACAtttactttaagacaattccaggcaaattata                                                                                                                 >  2:459031‑M2/1‑112 (MQ=255)                               aCGTTTATCATGTTATCCTAAGGATTATCCGAAAAATAATACCTACGAACATCTTCCAGGATACTCCTGCAGCGAAATATTTGTTTTAAGCTCACTCACATATCGCAACAtttactttaagacaattccaggcaaattataca                                                                                                               <  2:548187‑M2/143‑34 (MQ=255)                                   ttATCGTGTTATCCTAAGGATTATCCGAAAAATAATACCTACGAACATCTTCCAGGATACTCCTGCAGCGAAATATTTGTTTTAAGCTCACTCACATCTCGCAACAttaactttaagacaattccaggcaaataatacaaaac                                                                                                           <  1:129031‑M2/143‑38 (MQ=255)                                       cATGTAATCCTAAGGATTATCCGAAAAATAATACCTACGAACATCTTCCAGGATACTCCTGCAGCGAAATCTTTGTTTTAAGCTCACTCACATATCGCAACAtttactttaagacaattccaggcaaattatacaacacttta                                                                                                       <  1:595158‑M2/143‑42 (MQ=255)                                        aTGTTATCCTAAGGATTATCCGAAAAATAATACCTACGAACATCTTCCAGGATACTCCTGCAGCGAAATATTTGTTTTAAGCTCACTCACATATCGCAACAtttactttaagacaattccaggcaaattatacaacactttac                                                                                                      <  1:34623‑M2/143‑43 (MQ=255)                                         tGTTATCCTAAGGATTATCCGAAAAATAATACCTACGAACATCTTCCAGGATACTCCTGCAGCGAAATATTTGTTTTAAGCTCACTCACATATCGCAACAtttactttaagacaattccaggcaaattatacaacactttacg                                                                                                     >  2:234923‑M2/1‑100 (MQ=255)                                          gTTATCCTAAGGATTATCCGAAAAATAATACCTACGAACATCTTCCAGGATACTCCTGCAGCGAAATATTTGTTTTAAGCTCACTCACATATCGCAACAtttactttaagacaattccaggcaaattatacaacactttacgg                                                                                                    >  2:616993‑M2/1‑99 (MQ=255)                                                cTAAGGATTATCCGAAAAATAATACCTACGAACATCTTCCAGGATACTCCTGCAGCGAAATATTTGTTTTAAGCTCACTCACATATCGCAACAtttactttaagacactgcgaggcagagtatacaacactttacgggatagt                                                                                              <  2:297565‑M2/143‑51 (MQ=255)                                                 tAAGGATTATCCGAAAAATAATACCTACGAACATCTTCCAGGATACTCCTGCAGCGAAATATTTGTTTTAAGCTCACTCACATATCGCAACAtttcctttaagacaattcccggccaattatacatccctttcccgtatagtt                                                                                             <  2:189522‑M2/143‑52 (MQ=255)                                                  aaGGATTATCCGAAAAATAATACCTACGAACATCTTCCAGGATACTCCTGCAGCGAAATATTTGTTTTAAGCTCACTCACATATCGCAACAtttactttaagacaattccaggcaaattatacaacactttacgggatagtaa                                                                                            <  2:51257‑M2/143‑53 (MQ=255)                                                       ttATCCGAAAAATAATACCTACGAACATCTTCCAGGATACTCCTGCAGCGAAATATTTGTTTTAAGCTCACTCACATATAATACCCactacattaagacaattccaggcaaattatacaacactttacgggatagtaagtccg                                                                                       <  2:330259‑M2/143‑58 (MQ=255)                                                            cGAAAAATAATACCTACGAACATCTTCCAGGATACTCCTGCAGCGAAATATTTGTTTTAAGCTCACACACATATCGCAACAtttactttaagacacatccaggcaaattatacaacactttacgggatagtaagaccgcatga                                                                                  <  1:35689‑M2/143‑63 (MQ=255)                                                             gAAAAATAATACCTACGAACATCTTCCAGGATACTCCTGCAGCGAAATATTTGTTTTAAGCTCACTCACATATCGCAACAtttactttaagacaattccaggcaaattatacaacactttacgggctagtacgtccgcctgac                                                                                 <  2:252464‑M2/143‑64 (MQ=255)                                                              aaaaaTTATACCTACGAACATCTTCCAGGATACTCCTGCAGCGAAATATTTGTTTTAAGCTCACTCACATATCGCAACAtttactttaagacaattccaggcaaattatacaacactttacgggatagtaagtccgcctgaaa                                                                                >  1:298001‑M2/1‑79 (MQ=255)                                                              aaaaaTAATACCTACGAACATCTTCCAGGATACTCCTGCAGCGAAATATTTGTTTTAAGCTCACTCACATATCGCAACAtttactttaagacaattccaggcaaattatacaacactttacgggatagtaagtccgcctgaaa                                                                                >  1:240576‑M2/1‑79 (MQ=255)                                                              aaaaaTAATACCTACGAACATCTTCCAGGATACTCCTGCAGCGAAATATTTGTTTTAAGCTCACTCACATATCGCAACAtttactttaagacaattacaggcaaattatacaacactttacgagatagtgagtccgcatgaaa                                                                                <  1:426368‑M2/143‑65 (MQ=255)                                                                      tacctaccAACATCTTCCAGTATACTTCTGCAGCGAAATATTTGTTTTAAGCTCACTCACATATCGCAACAtttactttaagacaattccaggcaaattatacaacactttacgggatagtaagtccgcctgaaaaatcgcga                                                                        >  1:8610‑M2/1‑71 (MQ=255)                                                                      taCCTACGAACATCTTCCATGCTTCTCCTGCAGCGAAATATTTGTTTTAAGCTCACTCACATATCGCAACAtttactttaagacaattccaggcaaattatacaacactttacgggatagtaagtccgcctgaaaaatcgcga                                                                        >  1:41374‑M2/1‑71 (MQ=255)                                                                      taCCTACGAACATCTTCCACGATACTCCTGCAGCGAAATATTTGTTTTAAGTTGACTCACATATCGCAACAtttactttaagacaattccaggcaaattatacaacactttacgggatagtaagtccgcctgaaaaatcgcga                                                                        >  2:406574‑M2/1‑71 (MQ=255)                                                                      gacCTACGAACATCTTCCAGGATACTCCTGCAGCGAAATATTTGTTTTAAGCTCACTCACATATCGCAACAtttactttaagacaattccaggcaaattatacaacactttacgggatagtaagtccgcctgaaaaatcgcga                                                                        >  1:68553‑M2/2‑71 (MQ=255)                                                                          tACGAACATCTTCCAGGATACTCCTGCAGCGAAATATTTGTTTTAAGCTCACTCACATATCGCAACAtttactttaagacaattccaggcaaattatacaacactttacgggatagtaagtccgccagaaaaaacgcgagagt                                                                    <  1:629482‑M2/143‑77 (MQ=255)                                                                             gAACATCTTCCAGGATACTCCTGCAGCGAAATATTTGTTTTAAGCTCACTCACATATCGCAACAtttactttaagacaattccaggcaaattatacaacactttacgggatagtaagtccgcctgaaaaatcgcgagagtggc                                                                 >  1:188143‑M2/1‑64 (MQ=255)                                                                              aaCATCTTCCAGGATACTCCTGCAGCGAAATCTTTGTTTTAAGCTCACTCACATATCGCAACAtttagtttacgacaattccaggcaaattatacaacactttccggggtagtaaggccgcctgaagaaacgcgagagggggg                                                                <  2:302571‑M2/143‑81 (MQ=255)                                                                              aaCATCTTCCAGGATACTCCTGCAGCGAAATATTTGTTTTAAGCTCACTCACATATCGCAACAttgcatttaagacagttccaggcaaattatacaacactttagggggtagtaagtcagcttgtagaatggcgagagtggcg                                                                <  2:301936‑M2/143‑81 (MQ=255)                                                                                  tcggccacgcTACTCCTGCTGCCAAATATTTGTCTTGAGCTCACTCACATATCGCAACAtttactttagtacatttccaggcaaactatacaagcctttacgggatagtaagtccgcctgaaaaatcgcgagagtggcgcatt                                                            >  1:647487‑M2/5‑59 (MQ=255)                                                                                         ggATACTCCTGCAGCGAAATATTTGTTTTAAGCTCACTCACATATCGCAACAtttactttaagacaattccaggcaaattatacaacactttacgggatagtaagtccgcctgaaaaatcgcgagagtggcgcattaggtgac                                                     >  2:218845‑M2/1‑52 (MQ=255)                                                                                                 cTGCAGCGAAATATTTGTTTTAAGCTCACTCACATATCGCAACAtttactttaagacaattccaggcaaattatacaccactttacgggatagtacgtccgcctgaaaaatcgcgagcgtggcgcattaggcgacccaggttg                                             <  1:212673‑M2/143‑100 (MQ=255)                                                                                                       cGAAATATTTGTTTTAAGCTCACCCGCATATCGCAACAtttactttacgacaattccaggccaattatacaacactttactggatagtaagtccgcctgaaaaatcgcgagagtggcgcattaggtgacccatgttgttccgt                                       >  1:368211‑M2/1‑38 (MQ=255)                                                                                                        gAAATAATTGATTTAAGCTCACTCACATATCGCAACAtttactgtaagacaattccaggcaaattatacaacaatttacgggatagtaagtccgcctgaaaaatcgcgagaatggcgcattaggtgacccatgttgttccgtt                                      >  2:47168‑M2/1‑37 (MQ=255)                                                                                                          aaTATTTGTTTTAAGTTCACTCACATATCGCAACAtttactttaagacaattccaggcaaattatacaactctttacgggatagtaagtccgcctgaaaaatcgcgagagtggcgcattaggtgacccatgttgttccgttta                                    >  1:25052‑M2/1‑35 (MQ=255)                                                                                                              tttGTTTTAAGCTCACTCACATATCGCAACAtttactttaagacaattccaggcaaattatacaacactttacgggatagtaagtccgcctgaaaaatcgcgagagtggcgcattaggtgacccatgttgttccgtttagtca                                <  1:116756‑M2/143‑113 (MQ=255)                                                                                                                  ttttAAGCTCACTCACATATCGCAACAtttactttaagacaattccaggcaaattatacaacactttacgggatagtaagtccgcctgaaaaatcgcgagagtggcgcattaggtgacccatgttgttccgtttagtcatgat                            <  2:520258‑M2/143‑117 (MQ=255)                                                                                                                    ttAAGCTCACTCACATATCGCAACAtttactttaagacaattccaggcaaattatacaacactttacgggatagtaagtccgcctgaaaaatcgcgagagtggcgcattaggtgacccatgttgttccgcctagttattatgg                          <  2:59220‑M2/143‑119 (MQ=255)                                                                                                                             ctcacATATCGCAACAtttactttaagacaattccaggcaaattatacaacactttacgggatagtaagtccgcctgaaaaatcgcgagagtggcgcattaggtgacccatgttgttccgtttagtcatgatgaaatattcag                 >  1:189522‑M2/1‑16 (MQ=255)                                                                                                                             ctcacATATCGCAACAtttactttaagacaattccaggcaaattatacaacactttacgggatagtaagtccgcctgaaaaatcgcgagagtggcgcattaggtgacccatgttgttccgtttagtcatgatgaaatattcag                 >  2:43477‑M2/1‑16 (MQ=255)                                                                                                                              tcacATATCGCAACAtttactttaagacaattccaggcaaattatacaacactttacgggatagtaagtccgcctgaaaaatcgcgagagtggcgcattaggtgacccatgttgttccgtttagtcatgatgaagtatgcagg                <  1:679722‑M2/143‑129 (MQ=255)                                                                                                                                  atatCGCAACAtttactttaagacaattccaggcaaattatacaacactttacgggatagtaagtccgcctgaaaaatcgcgagagtggcgcattaggtgacccatgttgttccgtttagtcatgatgaaatattcaggtaag            <  1:318621‑M2/143‑133 (MQ=255)                                                                                                                                      cGCAACAtttactttaagacaattccaggcaaattatacaacactttacgggatagtaagtccgcctgaaaaatcgcgagagtggcgcattaggtgacccatggtgttacgacgagcccagatgaactagacagctaagggga        <  1:657010‑M2/143‑137 (MQ=255)                                                                                                                                      cGCAACActtactttaagacaattccaggcaaattatacaacactttacgggatagtaagtccgcctgaaaaatcgcgagagtggcgcattaggtgacccatgttgttccgtttagtcatgatgaaatattcaggtaagggga        >  2:291974‑M2/1‑7 (MQ=255)                                                                                                                                            atttactttaagacaattccaggcaaattatacaacactttacgggatagtaagtccgcctgaaaaatcgcgagagtggcgcattaggtgacccatgttgttccgtttagtcatgatgaaatattcaggtaaggggaattatc  >  2:34623‑M2/1‑1 (MQ=255)                                                                                                                                            |                                                                                                                                               TTAGTGAATTGCCATTAATATAATTCCGTAACGTTTATCATGTTATCCTAAGGATTATCCGAAAAATAATACCTACGAACATCTTCCAGGATACTCCTGCAGCGAAATATTTGTTTTAAGCTCACTCACATATCGCAACATTTACTTTACTTTAAGACAATTCCAGGCAAATTATACAACACTTTACGGGATAGTAAGTCCGCCTGAAAAATCGCGAGAGTGGCGCATTAGGTGACCCATGTTGTTCCGTTTAGTCATGATGAAATATTCAGGTAAGGGGAA  >  NC_000913/2023656‑2023937

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: ‑