Predicted mutation
evidence	seq id	position	mutation	freq	annotation	gene	description
RA	NC_000913	1,589,069	C→T	19.9%	pseudogene (1011/1227 nt)	ydeT ←	pseudogene; putative outer membrane protein

Read alignment evidence...
	seq id	position		ref	new	freq	score (cons/poly)	reads	annotation	genes	product
*	NC_000913	1,589,069	0	C	T	19.9%	132.5 / 8.0	62	pseudogene (1011/1227 nt)	ydeT	pseudogene; putative outer membrane protein
Reads supporting (aligned to +/- strand):  ref base C (41/8);  new base T (2/11);  total (43/19)
Fisher's exact test for biased strand distribution p-value = 8.48e-06
Kolmogorov-Smirnov test that lower quality scores support variant p-value = 1.00e+00

TAATCTATTGTTCCTTAGCGACAGATTGCTGTCTGCTGGTTCAGTAAGGTACCAGGAGAAACTTCAGGAAGCTTGTACTCGACAATACAGTTTGAGTTTTTATCTTTGCCCCATGAAACCTGTA‑ATTGCCCTGAC‑TGTGGAAGT‑CCAGTCAGATAAA‑CCTGACCATTTT‑CCGCG‑AC‑AATGCTGCCATTTTTATTCTCTCCGTGTGTGACAATTGCACCGAATGGAACGC‑TCTTATTACCGTACTTCAACGTCATTAATACTTTCCCGCCGATTTGTGCATTAAATGTTGCTCTGGCAATAGCACCGTGAGTTGGGATGACAGTGACCACGGTTTCATCCAGTTCAACATTATCTGCAAGGGAATTCGCGTTAAGAGCAACACGGTTTTCTCTATATTCTGTCGCAAATGGTAATATGGCATAGCCACGCCAGTCGGTATGAATTCCGGTCTGGTTCTCTATTTTGACA  >  NC_000913/1588839‑1589306                                                                                                                                                                                                                                               |                                                                                                                                                                                                                                              tAATCTTTTTTTCCTTAGCGACATATTGCTGTCTGCTGGTTCAGTAAGGTACCAGGAGAAACTTCAGGAAGCTTGTACTCGACAATACAGTTTGAGTTTTTATCTTTGCCCCATGAAACCTGTA‑ATTGCCCTGAC‑TGTGGAAGT‑CCAGTCAGATAAA‑CCTGACCATTTT‑CCGCG‑AC‑AATGCTGCCATTTTTATTCTCTCCGTGTGTGACAATTGCACCGAATGGAACGC‑TCTTATTAcc                                                                                                                                                                                                                                       <  2:1060097/239‑1 (MQ=255)      tATTGTTCCTTAGCGACAGATTGCTGTCTGCTGGTTCAGTAAGGTACCAGGAGAAACTTCAGGAAGCTTGTACTCGCCAATACAGTTTGAGTTTTTATCTTTGCCCCATGAAACCTGTA‑ATTGCCCTGAC‑TGTGGAAGT‑CCAGTCAGCTAAA‑CCTGACCATTTT‑CCCCG‑AC‑AATGCAGCCATTTTTATTCTCTCCGTGTGTGCCACTTGCACCGAATAGCACGC‑TCTTATTCCCGTACt                                                                                                                                                                                                                                  >  1:140749/1‑239 (MQ=255)         tGTTCCTTAGCGACAGATTGCTGTCTGCTGGTTCAGTAAGGTACCAGGAGAAACTTCAGGAAGCTTGTACTCGACAATACAGTTTGAGTTTTTATCTTTGCCCCATGAAACCTGTA‑ATTGCCCTGAC‑TGTGGAAGT‑CCAGTCAGATAAA‑CCTGACCATTTT‑CCGCG‑AC‑AATGCTGCCATTTTTATTCTCTCCGTGTGGGACAATTGCACCGAATGGACCGC‑TCTTATTACCGTCCTTCa                                                                                                                                                                                                                               >  1:119002/1‑239 (MQ=255)           ttCCTTAGCGACAGATTTCTTTCTGGTGGTTCAGTAAGGTACCATGAGAAACTTCAGGAAGCTTGTACTCGACAATGCAGTTTGAGTTTTTATCTTTGCCCCATGAAACCTGTA‑ATTGCCCTGAC‑TGTGGAAGT‑CCAGTCAGATAAA‑CCTGACCATTTT‑CCGCG‑AC‑AATGCTGCCATTTTTATTCTCTCCGTGTGTGACAATTGCACCGAATGGAACGC‑TCTTATTACCGTACTTCAAc                                                                                                                                                                                                                             <  2:304807/239‑1 (MQ=255)            tCCTTAGCGAAGGGTTGCGTGCGGCTGGTTCAGTAAGGTACCAGGAGAAACTTCAGGAAGCTTGGACTAGACAATACAGGTTGAGTTTTTAGCTTTGCCCCATGAAACCTGTA‑ATTGCCCTGAC‑TGTGGAAGT‑CCAGTCAGATAAA‑CCTGACCATTTT‑CCGCG‑AC‑AATGCTGCCATTTTTATTCTCTCCGTGTGTGACAATTGCACCGAATGGAACGC‑TCTTATTACCGTACTTCAAc                                                                                                                                                                                                                             <  1:799094/238‑1 (MQ=255)                tAGCGACAGATTGCTGTCTGCTGGTTCAGTAAGGTACCAGGTGAAACTTCAGGAAGCTTGTACTCGACCATACAGTTTGAGTTTTTATCTTTGCCCGATGAAACCTGTA‑ATTGCCCTGAC‑TGTGGAAGT‑CCAGTCAGATAAA‑ACTGCCCCTTTT‑ACGCG‑AC‑AATGCTGCCATTTATCTTCTCTCCGTGTGTGTCATTTGCCCCGAATGGAACGA‑CCTGTTTACCTAACTTCAACGACAt                                                                                                                                                                                                                        >  2:473002/1‑239 (MQ=255)                tAGCGACAGATTGCTGTCTGCTGGTTCAGTAAGGTACCAGGAGAAACTTCAGGAAGCTTGTACTCGACAATACAGTTTGAGTTTTTATCTTTGCCCCATGAAACCTGTA‑CTTGCCCTGAC‑TGTGGAAGT‑CCAGTCAGATAAA‑CCTGACCATTTT‑CCGCG‑CC‑AATGCTGCCATTTTTATTCTCTCCGTGTGTGACAATTGCACCGAATGGAACGC‑TTTTATTCCCGACATTCAACGTCAt                                                                                                                                                                                                                        >  2:330575/1‑239 (MQ=255)                tAGCGACAGATTGCTGTCTGCTGGTTCAGTAAGGTACCAGGAGAAACTTCAGGAAGCTTGTACTCGACAATACAGTTTGAGTTTTTATCTTTGCCCCATGAAACCTGTA‑ATTGCCCTGAC‑TGTGGAAGT‑CCAGTCAGATAAA‑CCTGACCATTTT‑CCGCG‑AC‑AATGCTGCCATTTTTATTCTCTCCGTGTGTGACAATTGCACCGAATGGAACGC‑TCTTATTCCCGTACTTTAACTTctt                                                                                                                                                                                                                        >  1:97847/1‑237 (MQ=255)                tAGCGACAGATTGCTGTCTGCTGGTTCAGTAAGGTACCAGGAGAAACTTCAGGAAGCTTGTACTCGACAATACAGTTTGAGTTTTTATCTTTGCCCCATGAAACCTGTA‑ATTGCCCTGAC‑TGTGGAAGT‑CCAGTCAGATAAA‑CCTGACCATTTT‑CCGCG‑AC‑AATGCTGCCATTTTTATTCTCTCCGTGTGTGACAATTGCACCGAATGGAACGC‑TCTTATTACCGTACTCCAACGTCAt                                                                                                                                                                                                                        >  1:1010288/1‑239 (MQ=255)                     aCAGATTGCTGTCTGCTGGTTCAGTAAGGTACCAGGAGAAACTTCAGGAAGCTTGTACTCGACAATACAGTTTGAGTTTTTATCTTTGCCCCATGAAACCTGTA‑ATTGCCCTGAC‑TGTGGAAGT‑CCAGTCAGATAAA‑CCTGACCATTTT‑CCGCG‑AC‑AATGCTGCCATTTTTATTCTCTCCGTGTGTGACAATTGCACCGAATGGAACGC‑TCTTATTACCGTACTTCAACGTCATTAATa                                                                                                                                                                                                                   >  1:291710/1‑239 (MQ=255)                     aCAGATTGCTGTCTGCTGGTTCAGTAAGGTACCAGGAGAAACTGCAGGAAGCTTGTACTCGAAAATACAGTTTGCGTTTTTATCTTTGCCCCATGAAACCTGTA‑ATTGCCCTGAC‑TGTGGAAGT‑CCAGTCAGATAAA‑CCTGACCATTTT‑CCGCA‑TC‑ATTTCTGCCTTTTTTATTATCTCCTCTTGGGCAAGTTGCACAGAATGGAACAC‑TTTTTTTACCTTCCTTCAAAGGCTTTaaca                                                                                                                                                                                                                   >  2:1118788/1‑237 (MQ=255)                             cTGTCTGCTGGTTCAGTAAGGTACCAGGAAAAATTTCAGGAAGTTTGTACGCGACAATACAGTTTGAGTTTTTATCTTTGCCCCATGAAACCTGTA‑ATTGCCTTGAC‑TGTGGAAGT‑CCAGTCAGATAAA‑CCTGACCTTTTT‑CCGCG‑AC‑AATGCTGCCATTTTTATTCTCTCCGTGTGTGACAATTGCACCGAATGGAACGC‑TCTTATTACCGTACTTCAACGTCATTAATACTTTCccg                                                                                                                                                                                                           <  1:194335/239‑1 (MQ=255)                                  tgctgGTTCAGTAAGGTACCAGGAGAAACTTCAGGAAGCTTGTACTCGACAATACAGTTTGAGTTTTTATCTTTGCCCCATGAAACCTGTA‑ATTGCCCTGAC‑TGTGGAAGT‑CCAGTCAGATAAA‑CCTGACCATTTT‑CCGCG‑AC‑AATGCTGCCATTTTTATTCTCTCCGTGTGTGACAATTGCACCGAATGGAACGC‑TCTTATTACCGTACTTCAACGTCATTAATACTTTCCCGCCGAt                                                                                                                                                                                                      >  1:462233/1‑239 (MQ=255)                                     tgGTTCAGTAAGGTACCAGGAGAAACTTCAGGAAGCTTGTACTCGACAATACAGTTTGAGTTTTTATCTTTGCCCCATGAAACCTGTA‑ATTGCCCTGAC‑TGTGGAAGT‑CCAGTCAGATAAA‑CCTGACCATTTT‑CCGCG‑AC‑AATGCTGCCATTTTTATTCTCTCCGTGTGTGCACATTGCACCGAATGGACCGC‑TCTTCTTACCGTACTTCACCGCCATTAAAACTTTCCCGCCGCTTtg                                                                                                                                                                                                   >  2:456555/1‑239 (MQ=255)                                       gTTCAGTAAGGTACCAGGAGAAACTTCAGGAAGCTTGTACTCGACAATACAGTTTGAGTTTTTATCTTTGCCCCATGAAACCTGTA‑ATTGCCCTGAC‑TGTGGAAGT‑CCAGTCAGATAAA‑CCTGACCATTTT‑CCGCG‑AC‑CATGCTGCCATTTTTATTCTCTCCGTGTGTGACAATTGCACCGAAGGGAACGC‑TCTTATTACCGGACTTCAAAGCAATTAATACTTTCcctccccttttg                                                                                                                                                                                                  >  2:1189404/1‑231 (MQ=255)                                                     cAGGAGAAACTTCAGGAAGCTTGTACTCGACAATACAGTTTGAGTTTTTATCTTTGCCCCATGAAACCTGTA‑ATTGCCCTGAC‑TGTGGAAGT‑CCAGTCAGATAAA‑CCTGACCATTTT‑CCGCG‑AC‑AATGCTGCCATTTTTATTCTCTCCGTGTGTGACAATTGCACCGAATGGAACGC‑TCTTATTACCGTACTTCAACGTCATTAATACTTTCCCGCCGATTTGTGCATTAAATGTTGct                                                                                                                                                                                   >  1:444848/1‑239 (MQ=255)                                                      aGGAGAAACTTCAGGAAGCTTGTACTCGACAATACAGTTTGAGTTTTTATCTTTGCCCCATGAAACCTGTA‑ATTGCCCTGCC‑TGTGGAAGT‑CCAGTCAGCTAAA‑CCTGACCATTTT‑CCGCG‑AC‑AATGCTGCCATTTTTATTCTCTCCGTGTGTGACAATTGCACCGAATGGAACGC‑TCTTATTACCGTCCTTCAACGTCATTAAAACTTTACCGCCGATTTGGACATTAAAAGTTActc                                                                                                                                                                                  >  2:555754/1‑239 (MQ=255)                                                       ggAGAAACTTCAGGAAGCTTGTACTCGACAATACAGTTTGAGTTTTTATCTTTGCCCCATGAAACCTGTA‑ATTGCCCGGAC‑TGTGGAAGT‑CCAGTCAGATAAA‑CCTGACCATTTT‑CCGCG‑AC‑AATGCTGCCAGTTTTATTCTATCCGTGTGTGACAATTGCACCAAATGGAACGC‑TCTTATTACTATACTTCAACGCCATTAACACTTTCACCCCGCTTTGTGCATTAAATGttcc                                                                                                                                                                                    >  2:770451/1‑234 (MQ=255)                                                             aCTTCAGGAAGCTTGTACTCGACAATACAGTTTGAGTTTTTATCTTTGCCCCATGAAACCTGTA‑ATTGCCCTGAC‑TGTGGAAGT‑CCAGTCAGATAAA‑CCTGACCATTTT‑CCCCG‑AC‑AATGCTGCCATTTTTATTCTCCCCCTGTGTGACAATTGCCCCGAATGGAACGC‑TCTTATTACCGTCCTTCAACGTCATTAATCCTTTCCCGCCGCTTTGTGATTTAAATGTTGTCCTGGaaaa                                                                                                                                                                           >  2:887152/1‑238 (MQ=255)                                                              cTTCAGGAAGCTTGTACTCGACAATACAGTTTGAGTTTTTATCTTTGCCCCATGAAACCTGTA‑ATTGCCCTGAC‑TGTGGAAGT‑CCAGTCAGATAAA‑CCTGACCATTTT‑CCGCG‑AC‑AATGCTGCCATTTTTATTCTCTCCGTGTGTGGCAATTGCACCGAATGGAACGC‑TCTTATTACCGTACTTCAACGTCATTAATACTTTCCCGCCGATTTGTGCATTAAATGTTGCTCTGGCAAt                                                                                                                                                                           >  1:745603/1‑238 (MQ=255)                                                                     aagtttttccccGAAAATACTGTTTGATTTTTTTTCTTTGCCCAATGAACCCTGTA‑ATTGCCCTGAT‑TGTGGAAGT‑CCAGTCAGATAAA‑CCTGACCTTTTT‑CCGGG‑AA‑AATGCTGCCTTTTTTATTCTCTCCGTGTGTGAAAATGGCACCGAATGGAACGC‑TTTTATTACCGTACTTCAACGTCATTAATACTTTCCCGCCGATTTGTGCATTAAATGTTGCTCTGGCAATAGCAcc                                                                                                                                                                     <  1:330575/226‑1 (MQ=255)                                                                                      tACAGTTTGAGTTTTTATCTTTGCCCCATGAAACCTGTA‑ATTGCCCTGAC‑TGTGGAAGT‑CCAGTCAGATAAA‑CCTGACCATTTT‑CCGCG‑AC‑AATGCTGCCATTTTTATTCTCTCCGTGTGTGACAATTGCACCGAATGGAACGC‑TCTTATTACCGTACTTCAACGTCATTAATACTTTCCCGCCGATTTGTGCCTTAAATGTTGCTCTGCCAATAGCACCGTGAGTTGGGCTGACAgga                                                                                                                                                  >  1:699635/1‑237 (MQ=255)                                                                                          ttttggttttttCTCTTTGCCCCAAGAAACCTGTA‑ATTGCCCTGAC‑TGTGGAATC‑CCAGTCAGATAAC‑CCGGCCCATTTC‑CCGGG‑AC‑AATGCTGCCTTTTTTATTCTCCCCGTGTGTGAAAATTGCCCCGAATGGAACGC‑TTTTATTACCGTACTTAACCGTCATTAATACTTTCCCGCCGATTTGTGCATTAAATGTTGCTCTGGCAATAGCACCGTGAGTTGGGATGACAGTGACCa                                                                                                                                              <  1:1189404/232‑1 (MQ=255)                                                                                           ttttgtttttttttttTGTCCCTTGAAACCTTTATATTCCCCT‑AC‑TGGGGAAATCCCTGTCATAAAAC‑CCTGCCTTTTTT‑CCGGG‑AA‑AATGCTGCTTTTTTTATTCTCTCGTTGTGTGACATTTGCCCCAAATGGACCGC‑TTTTTTTACCGTACTTCAACGTCATTAATCCTTCCCCGCCGATTTGTGCATTAAATGTTGCTCTGGCAATAGCACCGTGAGTTGGGATGACAGTGACCa                                                                                                                                              <  2:165916/233‑1 (MQ=255)                                                                                                   tttATCTTTGCCCCATGAAACCTGTA‑ATTGCCCTGAC‑TGTGGAAGT‑CCAGTCAGATAAA‑CCTGACCATTTT‑CCGCG‑AC‑AATGCTGCCATTTTTATTCTCTCCGTGTGTGACAATTGCACCGAATGGAACGC‑TCTTATTACCGTACTTCAAGGTCATTAATACTTTCCAGCCGATTTTTCCTTTAAATTTTGCCCTGCAAATACCACCGTGGCTTGGGATGACAGAGACACAGGTTTCac                                                                                                                                     >  2:524098/1‑238 (MQ=255)                                                                                                   tttATCTTTGCCCCATGAAACCTGTA‑ATTGCCCTGAC‑TGTGGAAGT‑CCAGTCAGATAAA‑CCTGACCATTTT‑CCGCG‑AC‑AATGCTGCCATTTTTATTCTCTCCGTGTGTGACAATTGCACCGAATGGAACGC‑TCTTATTACCGTACTTCAACGTCATTAATACTTTCCCGCCGATTTGTGCATTAAATGTTGCTCTGGCAATAGCACCGTGAGTTGGGATGACAGTGACCACGGTTTCa                                                                                                                                      >  1:1016377/1‑238 (MQ=255)                                                                                                     tttctcttccccATCAACCCCTTT‑ATTGCCCTGACTTGTGGAGTG‑CCAGACA‑ATAAACCCTGGCC‑TTTT‑CCGGC‑ACTAGGGCTGCCGTTTTTATTCGCTGCGTGTGTTACAATTCATCCGAATGG‑ACGCGTTATTTCCCCGTACTTCAGCCTCATTAATGCTTCCCCGCCGATTTGTGCATTAAATGTTGCTCTGGCAATAGCACCGTGAGTTGGGATGACAGTGACCACGGTTTCATc                                                                                                                                    <  2:444848/231‑1 (MQ=255)                                                                                                     tATCTTTGCCCCATGAAACCTGTA‑ATTGCCCTGAC‑TGTGGAAGT‑CCAGTCAGATAAA‑CCTGACCATTTT‑CCGCG‑AC‑AATGCTGCCATTTTTATTCTCTCCGTGTGTGACAATTGCACCGAATGGAACGC‑TCTTATTACCGTACTTCAACGTCATTAATACTTTCCCGCCGATTTTTGCATTAAATGTTGCTCTGGCAATATCACCGTGAGTTGGGCTGACATGGACCACGGTTTTATcc                                                                                                                                   >  2:100861/1‑239 (MQ=255)                                                                                                         ttgcccccAGAAAACCTGTA‑ATTGCCCTGCC‑TGTGGAATT‑CCGGTCAGATAAC‑CCTGCCCATTTC‑CCGCG‑AC‑AATGCTGCCATTTTTATTCTCTCCGTGTGTGACAATTGCACCGAATGGAACGC‑TCTTATTCCCGTACTTCAACGTCATTAATCCTTTCCCGCCGATTTGTGCATTAAATGTTGCTCTGGCAATAGCACCGTGAGTTGGGATGACAGTGACCACGGTTTCATCCAGtt                                                                                                                               <  1:664941/235‑1 (MQ=255)                                                                                                           tGCCCCATGAAACCTGTA‑ATTGCCCTGAC‑TGTGGAAGT‑CCAGTCAGATAAA‑CCTGACCATTTT‑CCGCG‑AC‑AATGCTGCCATTTTTATTCTCTCCGTGTGTGACAATTGCACCGAATGGAACGC‑TCTTATTACCGTACTTCAACGTCATTAATACTTTCCCGCCGATTTGTGCATTAAATGTTGCTCTGGCAATAGCACCGGGAGTTGGGTTGACAGTGACAAGGGTTTAATCCAGTTCa                                                                                                                             >  2:1026738/1‑239 (MQ=255)                                                                                                                                      gAC‑TGTGGAAGT‑CCAGTCAGATAAA‑CCTGACCATTTT‑CCGCG‑AC‑AATGCTGCCATTTTTATTCTCTCCGTGTGTGACAATTGCACCGAATGGAACGC‑TCTTATTACCGTACTTCAACGTCATTAATACTTTCCCGCCGATTTGTGCATTAAATGTTGCTCTGGCAATAGCACCGTGAGTTGGGATGACAGTGACCCCGGTTTCATCCAGTTCAACATTATCTGCACGGGAATTCGCGtt                                                                                                   >  1:226658/1‑239 (MQ=255)                                                                                                                                       aC‑TGTGGAAGT‑CCAGTCAGATAAA‑CCTGACCATTTT‑CCGCG‑AC‑AATGCTGCCATTTTTATTCTCTCCGTGTGTGACAATTGCACCGAATGGAACGC‑TCTTATTACCGTACTTCAACGTCATTAATACTTTCCCGCCGATTTGTGCATTAAATGTTGCTCTGGCAATAGCACCGTGAGTTGGGATGACAGTGACCACGGTTTCATCCAGTTCAACATTATCTGCAAGGGAATTCCCGTTa                                                                                                  >  1:1261971/1‑239 (MQ=255)                                                                                                                                             tggactttcggTCAAATAAA‑CCCTCCCATTTC‑CCGGC‑AA‑AATGCTGCAATTTTTATTCCCTCGGTGTGTAACAATTACACCGAATGGAACGC‑TCTTATTACCGTACTTCAACGTCATTAATACTTTCCCGCCGATTTGTGCATTAAATGTTGCTCTGGCAATAGCACCGTGAGTTGGGATGACAGTGACCACGGTTTCATCCAGTTCAACATTATCTGCAAGGGAATTCGCGTTAagag                                                                                              <  1:555754/229‑1 (MQ=255)                                                                                                                                             ggAAGT‑CCAGTCAGATAAA‑CCTGACCATTTT‑CCGCG‑AC‑AATGCTGCCATTTTTATTCTCTCCGTGTGTGACAATTGCACCGAATGGAACGC‑TCTTATTACCg                                                                                                                                                                                                                                      <  1:341290/102‑1 (MQ=255)                                                                                                                                             ggAAGT‑CCAGTCAGATAAA‑CCTGACCATTTT‑CCGCG‑AC‑AATGCTGCCATTTTTATTCTCTCCGTGTGTGACAATTGCACCGAATGGAACGC‑TCTTATTACCg                                                                                                                                                                                                                                      >  2:341290/1‑102 (MQ=255)                                                                                                                                                 tttttgatgttaTAAA‑CCTGAAC‑TTTT‑CCGGGTAC‑AGTGCTGCCTTTTTTATGCTTTCGTGGTGTGAAAATTCCACCGAATGGACCGC‑TTTGTGTGCCTTACTTCAACGTCATTAATCCTTTCCCGCCGATTTGTGCATTAAATGTTGCTCTGGCAATAGCACCGTGAGTTGGGATGACAGTGACCACGGTTTCATCCAGTTCAACATTATCTGCAAGGGAATTCGCGTTAAGAGCaa                                                                                           <  2:387304/227‑1 (MQ=255)                                                                                                                                                  t‑CCAGTCAGATAAA‑CCTGACCATTTT‑CCGCG‑AC‑AATGCTGCCATTTTTATTCTCTCCGTGTGTGACAATTGCACCGAATGGAACGC‑TCTTATTACCGTACTTCAACGTCATTAATACTTTCCCGCCGATTTGTGCATTAAATGTTGCTCTGGCAATAGCa                                                                                                                                                                       >  1:161469/1‑160 (MQ=255)                                                                                                                                                  t‑CCAGTCAGATAAA‑CCTGACCATTTT‑CCGCG‑AC‑AATGCTGCCATTTTTATTCTCTCCGTGTGTGACAATTGCACCGAATGGAACGC‑TCTTATTACCGTACTTCAACGTCATTAATACTTTCCCGCCGATTTGTGCATTAAATGTTGCTCTGGCAATAGCACCGTGAGTTGGGATGACAGTGACCACGGTTTCATCCAGTTCACCATTATCTGCAAGGGAATTCGCGTTAAGAGCAacac                                                                                        >  1:265162/1‑239 (MQ=255)                                                                                                                                                  t‑CCAGTCAGATAAA‑CCTGACCATTTT‑CCGCG‑AC‑AATGCTGCCATTTTTATTCTCTCCGTGTGTGACAATTGCACCGAATGGAACGC‑TCTTATTACCGTACTTCAACGTCATTAATACTTTCCCGCCGATTTGTGCATTAAATGTTGCTCTGGCAATAGCACCGTGAGTTGGGATGACAGTGACCACGGTTTCATCCAGTTCAACATTATCTGCAAGGGAATTCGCGTTAAGAGCAacac                                                                                        >  1:1211556/1‑239 (MQ=255)                                                                                                                                                     cAGTCAGATAAA‑CCTGACCATTTT‑CCGCG‑AC‑AATGCTGCCATTTTTATTCTCTCCGTGTGTGACAATTGCACCGAATGGAACGC‑TCTTATTACCGTACTTCAACGTCATTAATACTTTCCCGCCGATTTGTGCATTAAATGTTGCTCTGGCAATAGCACCGTGAGTTGGGTTGACAGTGACCACGGTTTCATCCAGTTCAACATTATCTGCAAGGGAATTCGCGTTAAGAGCAACACgg                                                                                      >  1:350137/1‑239 (MQ=255)                                                                                                                                                     cAGTCAGATAAA‑CCTGACCATTTT‑CCGCG‑AC‑AATGCTGCCATTTTTATTCTCTCCGTGTGTGACAATTGCACCGAATGGAACGC‑TCTTATTACCGTACTTCAACGTCATTAATACTTTCCCGCCGATTTGTGCATTAAATGTTGCTCTGGCAATAGCACCGTGAGTTGGGATGACAGTGACCACGGTTTCATCCAGTTCAACCTTATCTGCAAGGGAATTCGCGTTAAGGGCAACACgg                                                                                      >  1:852305/1‑239 (MQ=255)                                                                                                                                                     cAGTCAGATAAA‑CCTGACCATTTT‑CCGCG‑AC‑AATGCTGCCATTTTTATTCTCTCCGTGTGTGACAATTGCACCGAATGGAACGC‑TCTTATTACCGTACTTCAACGTCATTAATACTTTCCCGCCGATTTGTGCATTAAATGTTGCTCTGGCAATAGCACCGTGAGTTGGGATGACAGTGACCACGGTTTCATCCAGTTCAACATTATCTGCAAGGGAATTCGCGTTAAGAGCAACACgg                                                                                      >  1:1109957/1‑239 (MQ=255)                                                                                                                                                     cAGTCAGATAAA‑CCTGACCATTTT‑CCGCG‑AC‑AATGCTGCCATTTTTATTCTCTCCGTGTGTGACAATTGCACCGAAAGGAACGC‑TCTTATTACCGTACTTCAACGTCATTAATACTTTCCCGCCGCTTTGTGCATTAAATGTTGCTCTGGCAATAGCa                                                                                                                                                                       >  2:557852/1‑158 (MQ=255)                                                                                                                                                       gTCAGATAAA‑CCTGACCATTTT‑CCGCG‑AC‑AATGCTGCCATTTTTATTCTCTCCGTGTGTGACAATTGCACCGAATGGAACGC‑TCTTATTACCGTACTTCAACGTCATTAATACTTTCCCGCCGATTTGTGCATTAAATGTTGCTCTGGCAATAGCACCGTGAGTTGGGATGACAGTGACCACGGTTTCATCCAGTTCAACATTATCTGCAAGGGAATTCGCGTTAAGAGCAACACGGtt                                                                                    >  1:195031/1‑239 (MQ=255)                                                                                                                                                         cAGAAAAA‑CCTGACCTTTTT‑CCGCA‑AA‑AATGCTCCCTTTTTTATTCTCTCCGTGTGTGACAATTGCACCGAATGGAACGC‑TTTTATTACCGTACTTCAACGTCATTAATACTTCCCCGCCGATTTGTGCATTAAATGTTGCTCTGGCAATAGCACCGTGAGTTGGGATGACAGTGACCACGGTTTCATCCAGTTCAACATTATCTGCAAGGGAATTCGCGTTAAGAGCAACACGGttt                                                                                   <  1:1026738/238‑1 (MQ=255)                                                                                                                                                          aagtAAA‑ACTGGCCCTTTTCCCGGG‑AC‑AATGCTGCCTTTTTTATTCCCCCCGGGTGTGACAATTGCCCCGAATGGAACGC‑TTTTATTACCGTACTTCAACGTCATTAATACTTTCCCGCCGATTTGTGCATTAAATGTTGCTCTGGCAATAGCACCGTGAGTTGGGATGACAGTGACCACGGTTTCATCCAGTTCAACATTATCTGCAAGGGAATTCGCGTTAAGAGCAACACGGttt                                                                                   <  1:100861/235‑1 (MQ=255)                                                                                                                                                             tAAA‑CCTGACCATTTT‑CCGCG‑AC‑AATGCTGCCATTTTTATTCTCTCCGTGTGTGACAATTGCACCGAATGGAACGC‑TCTTATTACCGTACTTCAACGTCATTAATACTTTCCCGCCGATTTGTGCATTAAATGTTGCTCTGGCAATAGCACCGTGAGTTGGGATGACATTGACCACGGTTTCATCCAGTTCCACATTATTTGCAAGGGAATTCGGTTTAAGGGAAACACGGTTTTctct                                                                              >  2:1187489/1‑239 (MQ=255)                                                                                                                                                                     gACCATTTT‑CCGCG‑AC‑AATGCTGCCATTTTTATTCTCTCCGTGTGTGACAATTGCACCGAATGGAACGC‑TCTTATTACCGTACTTCAACGTCATTAATACTTTCCCGCCGATTTGTGCATTAAATGTTGCTCTGGCAATAGCACCGTGAGTTGGGATGACAGTGACCACGGTTTCATCCAGTTCAACATTATCTGCAAGGGAATTCGCGTTAAGAGCAACACGGTTTTTTCtata                                                                           >  1:962377/1‑235 (MQ=255)                                                                                                                                                                      aCCATTTT‑CCGCG‑AC‑AATGCTGCCATTTTTATTCTCTCCGTGTGTGACAATTGCACCGAATGGAACGC‑TCTTATTACCGTACTTCAACGTCATTAATACTTTCCCGCCGATTTGTGCATTAAATGTTGCTCTGGCAATAGCACCGTGAGTTGGGATGACAGTGACCACGGTTTCATCCAGTTCAACATTATCTGCCAGGGAATTCCCGTTACGAGCAACACGGTTTTCTCTTtcttct                                                                       >  1:679117/1‑238 (MQ=255)                                                                                                                                                                      aCCATTTT‑CCGCG‑AC‑AATGCTGCCATTTTTATTCTCTCCGTGCGTGACAATTGCACCGAATGGAACGC‑TCTTATTACCGTACTTCAACGTCATTAATACTTTCCCGCCGATTTGTGCATTAAATGTTGCTCTGGCAATAGCACCGTGAGTTGGGATGACCGTGACCACGGTTTCATCCAGTTCACCATTATCTGCAAGGGAATTCGCGTTAAGCGTAACACGGTTTTCTCTatat                                                                          >  1:357134/1‑235 (MQ=255)                                                                                                                                                                           ttt‑CCGGA‑AA‑AATGCTGCCTTTTTTTTTCCTGCCTTTGGGGATAATTGCACCGAAGGGAACTT‑TTTTATTACTGTACTGCAAGGTTATTAATTCTTTCCCGCCGATTTGTGCATTAAATGTTGCTCTGGCAATAGCACCGTGAGTTGGGATGACAGTGACCACGGTTTCATCCAGTTCAACATTATCTGCAAGGGAATTCGCGTTAAGAGCAACACGGTTTTCTCTATATTCTGTCGCa                                                                 <  2:195031/239‑1 (MQ=255)                                                                                                                                                                            ttcccGCG‑AA‑AATGTTGCCATTTTTATTCTCTCCGTGTGTGACAATTGCCCCGAATGGACCGC‑TTTTATTACCGTACTTCAACTTCATTAATACTTCCCCGCCGATTTGTGCATTAAATGTTGCTCTGGCAATAGCACCGTGAGTTGGGATGACAGTGACCACGGTTTCATCCAGTTCAACATTATCTGCAAGGGAATTCGCGTTAAGAGCATCACGGTTTTCTCTATATTCTGTCGCa                                                                 <  1:456555/236‑1 (MQ=255)                                                                                                                                                                             t‑CCGCG‑AC‑AATGCTGCCATTTTTATTCTCTCCGTGTGTGACAATTGCACCGAATGGAACGC‑TCTTATTACCGTACTTCAACGTCATTAATACTTTCCCGCCGATTTGTGCATTAAATGTTGCTCTGGCAATAGCACCGTGAGTTGGGATGACAGTGACCACGGTTTCATCCAGTTCAACATTATCTGCAAGGGAATTCGCGTTAAGAGCAAAACGGTTTTCTCTAAATTCTTTGGCaaa                                                               >  2:1187108/1‑239 (MQ=255)                                                                                                                                                                                                    tttATTCTCTCCGTGTGTGACAATTGCACCGAATGGAACGC‑TCTTATTACCGTACTTCAACGTCATTAATACTTTCCCGCCGATTTGTGCATTAAATGTTGCTCTGGCAATAGCACCGTGAGTTGGGATGACAGTGACCACGGTTTCATCCAGTTCAACATTATCTGCAAGGGAATTCGCGTTAAGAGCAACACGGTTTTCTCTATATTCTGTCGCAAATGGTAata                                                       >  1:365582/1‑227 (MQ=255)                                                                                                                                                                                                           tctcCGTTGTTGAAAATTGCACCGAATGGAACCT‑TCTTATTCCCTTACTTCAACGTCATTAATCCTTCCCCGCCGATTTGTGCATTAAATGTTGCTCTGGCAATAGCACCGTGAGTTGGGATGACAGTGACCACGGTTTCATCCAGTTCAACATTATCTGCAAGGGAATTCGCGTTAAGAGCAACACGGTTTTCTCTATATTCTGTCGCAAATGGTAATATGGCATAGCCACGCCAGTc                                    <  1:887152/239‑1 (MQ=255)                                                                                                                                                                                                             tcCGTGTGTGACAATTGCACCGAATGGAACGC‑TCTTATTACCGTACTTCAACGTCATTAATACTTTCCCGCCGATTTGTGCATTAAATGTTGCTCTGGCAATAGCACCGTGAGTTGGGATGACAGTGACCACGGTTTCATCCAGTTCAACATTATCTGCAAGGGAATTCGCGTTAAGAGCAACACGGTTTTCTCTATATTCTGTCGCAAATGGTAATATGGCATAGCCACGCCAGTCgg                                  >  1:72656/1‑239 (MQ=255)                                                                                                                                                                                                                          aTTGCACGGAAGGGAACGT‑TTTTATTCCCGTCCGTAAATCGATTTAATTTTTCCCCGCCGATTTGTGCATTAAATGTTGCTCTGGCAATAGCACCGTGAGTTGGGATGACAGTGACCACGGTTTCATCCAGTTCAACATTATCTGCAAGGGAATTCGCGTTAAGAGCAACACGGTTTTCTCTATATTCTGTCGCAAATGGTAATATGGCATAGCCACGCCAGTCGGTATGAATTCCGGt                     <  1:1187108/239‑1 (MQ=255)                                                                                                                                                                                                                           ttGCCCCGAGTGGAACGT‑CTTTTTTTCCGTACTTTAAGGTAATTAATCTTTTCCCGCCGATTTGTGCATTAAATGTTGCTCTGGCAATAGCACCGTGAGTTGGGATGACAGTGACCACGGTTTCATCCAGTTGAACATTATCTGCAAGGGAATTCGCGTTAAGAGCAACACGGTTTTCTCTATATTCTGTCGCAAATGGTAATATGGCATAGCCACGCCAGTCGGTATGAATTCCGGTc                    <  1:175974/239‑1 (MQ=255)                                                                                                                                                                                                                           ttGCACCGAATGGAACGC‑TCTTATTACCGTACTTCAACGTCATTAATACTTTCCCGCCGATTTGTGCATTAAATGTTGCTCTGGCAATAGCACCGTGAGTTGGGATGACAGTGACCACGGTTTCATCCAGTTCAACATTATCTGCAAGGGAATTCGCGTTAAGAGCAACACGGTTTTCTCTATATTCTGTCGCAAATGGTAATATGGCATAGCCACGCCAGTCGGTATGAATTCCgg                      >  1:535503/1‑237 (MQ=255)                                                                                                                                                                                                                                   aaTGGAACGC‑TCTTATTACCGTACTTCAACGTCATTAATACTTTCCCGCCGATTTGTGCATTAAATGTTGCTCTGGCAATAGCACCGTGAGTTGGGATGACAGTGACCACGGTTTCATCCAGTTCAACATTATCTGCAAGGGAATTCGCGTTAAGAGCAACACGGTTTTCTCTATATTCTGTCGCAAATGGTAATATGGCATAGCCACGCCCGTTGGTTTGAATTCCGGTTTGGGtc              >  2:868086/1‑237 (MQ=255)                                                                                                                                                                                                                                   aaTGGAACGC‑TCTTATTACCGTACTTCAACGTCATTAATACTTTCCCGCCGATTTGTGCATTAAATGTTGCTCTGGCAATAGCACCGTGAGTTGGGATGACAGTGACCACGGTTTCATCCAGTTCAACATTATCTGCAAGGGAATTCGCGTTAAGAGCAACACGGTTTTCTCTATATTCTGTCGCAAATGGTAATATGGCATAGCCACGCCAGTCGGTATGAAtt                          >  1:338717/1‑225 (MQ=255)                                                                                                                                                                                                                                   aaTGGAACGC‑TCTTATTACCGTACTTCAACGTCATTAATACTTTCCCGCCGATTTGTGCATTAAATGTTGCTCTGGCAATAGCACCGTGAGTTGGGATGACAGTGACCACGGTTTCATCCAGTTCAACATTATCTGCAAGGGAATTCGCGTTAAGAGCAACACGGTTTTCTCTATATTCTGTCGCAAATGGTAATATGGAAAAGCCACGCCAGTCGGAATAAATTCCGGTTTGGGtctc            >  2:164148/1‑239 (MQ=255)                                                                                                                                                                                                                                              tctTATTACCGTACTTCAACGTCATTAATACTTTCCCGCCGATTTGTGCATTAAATGTTGCTCTGGCAATAGCACCGTGAGTTGGGATGACAGTGACCACGGTTTCATCCAGTTCAACATTATCTGCAAGGGAATTCGCGTTAAGAGCAACACGGTTTTCTCTATATTCTGTCGCAAATGGTAATATGGCATAGc                                              >  1:1145229/1‑195 (MQ=255)                                                                                                                                                                                                                                              tctTATTACCGTACTTCAACGTCATTAATACTTTCCCGCCGATTTGTGCATTAAATGTTGCCCTGGCAATAGCACCGTGAGTTGGGATGACAGTGACCACGGTTTCATCCAGTTCAACATTATCTGCAAGGGAATTCGCGTTAACAGCAACAAGGTTTTCTCTATATTCTTTCGCAAATGGCAATATGGCATAGCCACGCCCTCCGGTATGAATTCCGGTCTGGTTTTCTATTTTGaaa  >  2:380173/1‑237 (MQ=255)                                                                                                                                                                                                                                               |                                                                                                                                                                                                                                              TAATCTATTGTTCCTTAGCGACAGATTGCTGTCTGCTGGTTCAGTAAGGTACCAGGAGAAACTTCAGGAAGCTTGTACTCGACAATACAGTTTGAGTTTTTATCTTTGCCCCATGAAACCTGTA‑ATTGCCCTGAC‑TGTGGAAGT‑CCAGTCAGATAAA‑CCTGACCATTTT‑CCGCG‑AC‑AATGCTGCCATTTTTATTCTCTCCGTGTGTGACAATTGCACCGAATGGAACGC‑TCTTATTACCGTACTTCAACGTCATTAATACTTTCCCGCCGATTTGTGCATTAAATGTTGCTCTGGCAATAGCACCGTGAGTTGGGATGACAGTGACCACGGTTTCATCCAGTTCAACATTATCTGCAAGGGAATTCGCGTTAAGAGCAACACGGTTTTCTCTATATTCTGTCGCAAATGGTAATATGGCATAGCCACGCCAGTCGGTATGAATTCCGGTCTGGTTCTCTATTTTGACA  >  NC_000913/1588839‑1589306

Alignment Legend
Aligned base mismatch/match (shaded by quality score): ATCG/ATCG < 3 ≤ ATCG/ATCG < 13 ≤ ATCG/ATCG < 14 ≤ ATCG/ATCG < 29 ≤ ATCG/ATCG < 39 ≤ ATCG/ATCG
Unaligned base: atcg    Masked matching base: atcg    Alignment gap: ‑    Deleted base: ‑