Predicted mutation
evidence	seq id	position	mutation	annotation	gene	description
RA	NC_000913	1,428,978	G→A	pseudogene (183/189 nt)	lomR →	Rac prophage; protein LomR_1

Read alignment evidence...
	seq id	position		ref	new	freq	score (cons/poly)	reads	annotation	genes	product
*	NC_000913	1,428,978	0	G	A	100.0%	103.5 / NA	30	pseudogene (183/189 nt)	lomR	Rac prophage; protein LomR_1
Reads supporting (aligned to +/- strand):  ref base G (0/0);  new base A (6/24);  total (6/24)

TAACCCGACCGAATCCGTGGCCATTGATATTGCTTATGAAGGCCCCGGCAGTGGCGACTGGCGCACTGACGGTTTCATCG‑TGGGTGTCGGTTATAAGTTCTGATTAGCCAGGTAACACAGTGTTATGACAGCCCGCCGGTTCAGGCGGGCTTTTTTGTGGGGTGAATATGGCAGTAAAGATTTCAGGTGTACTGAAAGACGGCACAGGAAAACCGGTACAGAACTGCACAATCCAGCTGAAAGCAAAACGTAACAGCACCACGGTGGTGGTGAACA‑CGCTGGCCTCAGAAAATCCGGATGAAGCCGGGCGTTACAGCATGGACGTTGAGTACGGTCAGTACAGCGTTATTCTGTTGGTGGAAGGATTCCCGC  >  NC_000913/1428882‑1429253                                                                                                  |                                                                                                                                                                                                                                                                                     taatcctgcagcgtccgtcgttgttGATATTGCTTATGAAGGCTCCGGCAGTGGCGACTGGCGTACTGACGGATTCATCGGTGGG‑GTCGGTTATAAATTCTGATTAGCCNGGTAACACAGTGTTATGACAGCCCGCCGGAACCGGGGGGCTTTTTTGTGGGGTGAATATGGCAGTAAAGATTTCAGGAGTCCTGAAAGACGGCACAGGAAAACCGGTACAGAACTGCACCATTCAGCTGAAAGCCAGACGTAACAACACCACGTTGGTGGTGAACA‑CGGTGGGCTCAGAGAATCCGGATg                                                                          <  1:556687/277‑1 (MQ=255)            cgtccgtcgttgttGATATTGCTTATGAAGGCTCCGGCAGTGGCGACTGGCGTACTGACGGATTCATCG‑TTGGGGTCGGTTATAAATTCTGATTAGCCAGGTAACACAGTGTTATGACAGCCCGCCGGAACCGGTGGGCTTTTTTGTGGGGTGAATATGGCAGTAAAGATTTCAGGAGTCCTGAAAGACGGCACAGGAAAACCGGTACAGAACTGCACCATTCAGCTGAAAGCCAGACGTAACAGCACCACGGTGGTGGTGAACA‑CGGTGGGCTCAGAGAATCCGGATGAAGCCGGGCGt                                                               >  1:657768/13‑300 (MQ=255)                 gtcgttgttGATATTGCTTATGAAGGCTCCGGCAGTGGCGACTGGCGTACTGACGGATTCATCG‑TTGGGGTCGGTTATAAATTCTGATTAGCCAGGTAACACAGTGTTATGACAGCCCGCCGGAACCGGTGGGCTTTTTTGTGGGGTGAATATGGCAGTAAAGATTTCAGGAGTCCTGAAAGACGGCACAGGAAAACCGGTACAGAACTGCACCATTCAGCTGAAAGCCAGACGTAACAGCACCACGGTGGTGGTGAACA‑CGGTGGGCTCAGAGAATCCGGATGAAGCCGGGCGTTACAg                                                          <  2:434451/293‑1 (MQ=255)                  tcgttgttGATATTGCTTATGAAGGCTCCGGCAGTGGCGACTGGCGTACTGACGGATTCATCG‑TTGGGGTCGGTTATAAATTCTGATTAGCCAGGTAACACAGTGTTATGACAGCCCGCCGGAACCGGTGGGCTTTTTTGTGGGGTGAATATGGCAGTAAAGATTTCCGGAGTCCTGAAAGACGGCACAGGAAAACCGGTACAGAACTGCACCATTCAGCTGAAAGCAAGACGTAACAGCACCACGGTGGTGGTGAACA‑CGGTGGGCTCAGAGAATCCGGATGAAGCCGGGCGTTACAGc                                                         >  1:290702/7‑300 (MQ=255)                    gttgttGATATTGCTTATGAAGGCTCCGGCAGTGGCGACTGGCGTACTGACGGATTCATCG‑TTGGGGTCGGTTATAAATTCTGATTAGCCAGGTAACACAGTGTTATGACAGCCCGCCGGAACCGGTGGGCTTTTTTGTGGGGTGAATATGGCAGTAAAGATTTCAGGAGTCCTGAAAGACGGCACAGGAAAACCGGTACAGAACTGCACCATTCAGCTGAAAGCCAGACGTAACAGCACCACGGTGGTGGTGAACA‑CGGTGGGCTCAGAGAATCCGGATGAAGCCGGGCGTTACAGCAt                                                       <  2:217894/296‑1 (MQ=255)                         tGATATTGCTTATGAAGGCTCCGGCAGTGGCGACTGGCGTACTGACGGATTCATCG‑TTGGGGTCGGTTAGAAATTCTGATTAGCCAGGTAACACAGTGTTATGACAGCCCGCCGGAACCGGTGGGCTTTTTTGTGGGTTGAATATGGCAGTAAAGATTTCAGGAGTCCTGAAAGACGGCACAGGAAAACCGGTACAGAACTGCACCATTCAGCTGAAAGCCAGACGTAACAGCACCACGGTGGTGGTGAACA‑CGGTGGGCTCAGAGAATCCGGATGAAGCCGGGCGTTACAGCATGGatg                                                  <  1:373905/300‑3 (MQ=255)                              ttGCTTATGAAGGCTCCGGCAGTGGCGACTGGCGTACTGACGGATTCATCG‑TTGGGGTCGGTTATAAATTCTGATTAGCCAGGTAACACAGTGTTATGACAGCCCNCCGGAACCGGTGGGCTTTTTTGTGGGGTGAATATGGCAGTAAAGATTTCAGGAGTCCTGAAAGACGGCACAGGAAAACCGGTACAGAACTGCACCATTCAGCTGAAAGCCAGACGTAACAGCACCACGGTGGTGGTGAACA‑CGGTGGGCTCAGAGAATCCGGATGAAGCCGGGCGTTACAGCATGGatgtggag                                             <  2:662797/300‑8 (MQ=255)                                gCTTATGAAGGCTCCGGCAGTGGCGACTGGCGTACTGACGGATTCATCG‑TTGGGGTCGGTTATAAATTCTGATTAGCCAGGTAACACAGTGTTATGACAGCCCGCCGGAACCGGTGGGCTTTTTTGTGGGGTGAATATGGCAGTAAAGATTTCAGGAGTCCTGAAAGACGGCACAGGAAAACCGGTACAGAACTGCACCATTCAGCTGAAAGCCAGACGTAACAGCACCACGGTGGTGGTGAACA‑CGGTGGGCTCCGAGAATCAGGATGAAGCAGGGCGTTACAGCATggctgtggagta                                           >  2:199491/1‑290 (MQ=255)                                gCTTATGAAGGCTCCGGCAGTGGCGACTGGCGTACTGACGGATTCATCG‑TTGGGGTCGGTTATAAATTCTGATTAGCCAGGTAACACAGTGTTATGACAGCCCGCCGGAACCGGTGGGCTTTTTTGTGGGGTGAATATGGCAGTAAAGATTTCAGGAGTCCTGAAAGACGGCACAGGAAAACCGGTACAGAACTGCACCATTCAGCTGAAAGCCAGACGTAACAGCACCACGGTGGTGGTGAACA‑CGGTGGGCTCAGAGAATCCGGATGAAGCCGGGCGTTACAGCATGGATGTGGAGTa                                           >  1:458372/1‑300 (MQ=255)                                gCTTATGAAGGCTCCGGCAGTGGCGACTGGCGTACTGACGGATTCATCG‑TTGGGGTCGGTTATAAATTCTGATTAGCCAGGTAACACAGTGTTATGACAGCCCGCCGGAACCGGTGGGCTTTTTTGTGGGGTGAATATGGCAGTAAAGATTTCAGGAGTCCTGAAAGACGGCACAGGAAAACCGGTACAGAACTGCACCATTCAGCTGAAAGCCAGAAGTAACAGCACCACGGTGGTGGTGAACA‑CGGTGGGCTCAGAGAATCCGGATGAAGCAGGGCGTTAAAGCATGGATGTGGAGTa                                           >  2:359595/1‑300 (MQ=255)                                    aTGAAGGCTCCGGCAGTGGCGACTGGCGTACTGACGGATTCATCG‑TTGGGGTCGGTTATAAATTCTGATTAGCCAGGTAACACAGTGTTATGACAGCCCGCCGGAACCGGTGGGCTTTTTTGTGGGGTGAATATGGCAGTAAAGATTTCAGGAGTCCTGAAAGACGGCACAGGAAAACCGGTACAGAACTGCACCATTCAGCTGAAAGCCAGACGTAACAGCACCACGGTGGTGGTGAACA‑CGGTGGGCTCAGAGAATCCGGATGAAGCCGGGCGTTACAGCATGGATGTGGAGTACGGt                                       <  1:340369/300‑1 (MQ=255)                                          gctccGGCAGTGGCGACTGGCGTACTGACGGATTCATCG‑TTGGGGTCGGTTATAAATTCTGATTAGCCAGGTAACACAGTGTTATGACAGCCCGCCGGAACCGGTGGGCTTTTTTGTGGGGTGAATATGGCAGTAAAGATTTCAGGAGTTCTGAAAGACGGCACAGGAAAACCGGTACAGAACTGCACCATTCAGCTGAAAGCCAGACGTAACAGCACCACGGTGGTGGTGAACA‑CGGTGGGCTCAGAGAATCCGGATGAAGCCGGGCGTTACAGCATGGATGTGGAGTACGGTCAGTAc                                 <  1:40836/297‑1 (MQ=255)                                          gctccGGCAGTGGCGACTGGCGTACTGACGGATTCATCG‑TTGGGGTCGGTTATAAATTCTGATTAGCCAGGTAACACAGTGTTATGACAGCCCGCCGGAACCGGTGGGCTTTTTTGTGGGGTGAATATGGCAGTAAAGATTTCAGGAGTCCTGAAAGACGGCACAGGAAAACCGGTACAGAACTGCACCATTCAGCTGAAAGCCAGACGTAACAGCACCACGGTGGTGGTGAACA‑CGGTGGGCTCAGAGAATCCGGATGAAGCCGGGCGTTACAGCATGGATGTGGAGTACGGTCAGTAc                                 <  1:34652/297‑1 (MQ=255)                                           ctccGGCAGTGGCGACTGGCGTACTGACGGATTCATCG‑TTGGGGTCGGTTATAAATTCTGATTAGCCAGGTAACACAGTGTTATGACAGCCCGCCGGAACCGGTGGGCTTTTTTGTGGGGTGAATATGGCAGTAAAGATTTCAGGAGTCCTGAAAGACGGCACAGGAAAACCGGTACAGAACTGCACCACTCAGCTGAAAGCCAGACGTAACAGCACCACGGTGGTGGTGAACA‑CGGTGGGCTCAGAGAATCCGGATGAAGCCGGGCGTTACAGCATGGATGTGGAGTACGGTCAGTACa                                >  2:8173/3‑300 (MQ=255)                                             ccGGCAGTGGCGACTGGCGTACTGACGGATTCATCG‑TTGGGGTCGGTTATAAATTCTGATTAGCCAGGTAACACAGTGTTATGACAGCCCGCCGGAACCGGTGGGCTTTTTTGTGGGGTGAATATGGCAGTAAAGATTTCAGGAGTCCTGAAAGACGGCACAGGAAAACCGGTACAGAACTGCACCATTCAGCTGAAAGCCAGACGTAACAGCACCACGGTGGTGGTGAACA‑CGGTGGGCTCAGAGAATCCGGATGAAGCCGGGCGTTACAGCATGGATGTGGAGTACGGTCAGTACAgt                              <  1:616740/300‑2 (MQ=255)                                               tgcattGGCGACTGGCGTACTGACGGATTCATCG‑TTGGGGTCGGTTATAAATTCTGATTAGCCAGGTAACACAGTGTTATGACAGCCCGCCGGAACCGGTGGGCTTTTTTTTGGGGTGAATATGGCAGTAAAGATTTCAGGAGTCCTGAAAGACGGCACAGGAAAACCGGTACAGAACTACACCATTCAGCTGAAAGCCAGACGTAACAGCACCAAGGAGGTGGTGGATATCG‑TGGGCTCGGAGAATCCGGATGAAGCCGGGCGTTACAGCATGGATGTGGAGTACGGTCAGTACAgtgt                            <  1:638999/295‑4 (MQ=255)                                               ggCAGTGGCGACTGGCGTACTGACGGATTCATCG‑TTGGGGTCGGTTATAAATTCTGATTAGCCAGGTAACACAGTGTTATGACAGCCCGCCGGAACCGGTGGGCTTTTTTGTGGGGTGAATATGGCAGTAAAGATTTCAGGAGTCCTGNAAGACGGCACAGGAAAACCGGTACAGNACTGCACCATTCAGCTGAAAGCCAGACGTAACAGCACCACGGTGGTGGTGAACA‑CGGTGGGCTCAGAGAATCCGGATGAAGCCGGGCGTTACAGCATGGATGTGGAGTACGGTCAGTACAgtgt                            <  2:519519/300‑4 (MQ=255)                                               ggCAGTGGCGACTGGCGTACTGACGGATTCATCG‑TTGGGGTCGGTTATAAATTCTGATTAGCCAGGTAACACAGTGTTATGACAGCCCGCCGGAACCGGTGGGCTTTTTTGTGGGGTGAATATGGCAGTAAAGATTTCAGGAGTCCTGAAAGACGGCACAGGAAAACCGGTACAGAACTGCACCATTCAGCTGAAAGCCAGACGTAACAGCACCACGGTGGTGGTGAACA‑CGGTGGGCTCAGAGAATCCGGATGAAGCCGGGCGTTACAGCATGGATGTGGAGTACGGTCAGTACAgtgt                            <  1:306996/300‑4 (MQ=255)                                               ggCAGTGGCGACTGGCGTACTGACGGATTCATCG‑TTGGGGTCGGTTATAAATTCTGATTAGCCAGGTAACACAGTGTTATGACAGCCCGCCGGAACCGGTGGGCTTTTTNGTGGGGTGAATATGGCAGTAAAGATTTCAGGAGTCCTGAAAGACGGCACAGGAAAACCGGTACAGAACTGCACCATTCAGCTGAAAGCCAGACGTAACAGCACCACGGTGGTGGTGAACA‑CGGTGGGCTCAGAGAATCCGGATGAAGCCGGGCGTTACAGCATGGATGTGGAGTACGGTCAGTACAgtgt                            <  1:516711/300‑4 (MQ=255)                                               ggCAGTGGCGACTGGCGGACTGACGGATTCATTG‑TTGGGGTCGGTTATAAATTCTGATTAGCCAGTTAACACAGTGTTATGACAGCCCGCCGGAACCGGTGGGCTTTTTTGTGGGGTGAATATGGCAGTAAAGATTTCAGGAGTCCTGAAAGACGGCACAGGAAAACCGGTACAGAACTGCACCATTCAGCTGAAAGCCAGACGTAACAGCACCACGGTGGTGGTGAACA‑CGGTGGGCTCAGAGAATCCGGATGAAGCCGGGCGTTACAGCATGGATGTGGAGTACGGTCAGTACAgtgt                            <  1:638992/300‑4 (MQ=255)                                                    tGGCGACTGGCGTACTGACGGATTCATCG‑TTGGGGTCGGTTATAAATTCTGATTAGCCAGGTAACACAGTGTTATGACAGCCCGCCGGAACCGGTGGGCTTTTTTGTGGGGTGAATATGGCAGTAAAGATTTCAGGAGTCCTGAAAGACGGCACAGGAAAACCGGTACAGAACTGCACCATTCAGCTGAAAGCCAGACGTAACAGCACCACGGTGGTGGTGAACA‑CGGTGGGCTCAGAGAATCCGGATGAAGCCGGGCGTTACAGCATGGATGTGGAGTACGGTCAGTACAgtgtcatcc                       <  1:130982/300‑9 (MQ=255)                                                      gCGACTGGCGTACTGACGGATTCATCG‑TTGGGGTCGGTTATAAATTCTGATTAGCCAGGTAACACAGTGTTATGACAGCCCGCCGGAACCGGTGGGCTTTTTTGTGGGGNGAATATGGCAGTAAAGATTTCAGGAGTCCTGAAAGACGGCACAGGAAAACCGGTACAGAACTGCACCATTCAGCTGAAAGCCAGACGTAACAGCACCACGGTGGTGGTGAACA‑CGGTGGGCTCAGAGAATCCGGATGAAGCCGGGCGTTACAGCATGGATGTGGAGTACGGTCAGTACAgtgtcatcctg                     <  1:539376/300‑11 (MQ=255)                                                      gCGACTGGCGTACTGACGGATTCATCG‑TTGGGGTCGGGTATAAATTCTGATTAGCCAGGTAACACAGTGTTATGACAGCCCGCCGGAACCGGTGGGCTTTTTTGGGGGGTGAATATGGCAGTAAAGATTTCAGGAGTCCTGAAAGACGGCACAGGAAAACCGGTACAGAACTGCACCATTCAGCTGAAAGCCAGACGTAACAGCACCACGGTGGTGGTGAACA‑CGGTGGGCTCAGAGAATCCGGATGAAGCCGGGCGTTACAGCATGGATGTGGAGTACGGTCAGTatagtgtcatcctg                     <  1:703332/300‑14 (MQ=255)                                                                  cTGACGNATTCATCG‑TTGTGGTCGGGTATAAATTTTGATTAGCCAGGTAACACANTGTTATGACAGCCCGCCGGAACCGGTGGGCTTTTTTGTGGGGTGAATATGGCAGTAAAGATTTCAGGAGTCCTGAAAGACGGCACAGGAAAACCGGTACAGAACTGCACCATTCAGCTGAAAGCCAGACGTAACAGCACCACGGTGGTGGTGAACA‑CGGTGGGCTCAGAGAATCCGGATGAAGCCGGGCGTTACAGCATGGATGTGGAGTACGGTCAGTACAgtgtcatcctgcaggttgacggt         <  2:631389/300‑23 (MQ=255)                                                                  cTGACGGATTCATCG‑TTGGGGTCGGTTATAAATTCTGATTAGCCAGGTAACACAGTGTTATGACAGCCCGCCGGAACCGGTGGGCTTTTTTGTGGGGTGAATATGGCAGTAAAGATTTCAGGAGTCCTGAAAGACGGCACAGGAAAACCGGTACAGAACTGCACCATTCAGCTGAAAGCCAGACGTAACAGCACCACGGTGGTGGTGAACA‑CGGTGGGCTCAGAGAATCCGGATGAAGCCGGGCGTTACAGCATGGATGTGGAGTACGGTCAGTAcctgtctcttatacacatctcgcag         <  1:439326/300‑25 (MQ=255)                                                                  cTGACGGATTCATCG‑TTGGGGTCGGTTATAAATTCTGATTAGCCAGGTAACACAGTGTTATGACAGCCCGCCGGAACCGGTGGGCTTTTTTGTGGGGTGAATATGGCAGTAAAGATTTCAGGAGTCCTGAAAGACGGCACAGGAAAACCGGTACAGAACTGCACCATTCAGCTGAAAGCCAGACGTAACAGCACCACGGTGGTGGTGAACA‑CGGTGGGCTCAGAGAATCCGGATGAAGCCGGGCGTTACAGCATGGATGTGGAGTACGGTCAGTACAgtgtcatcctgcaggttgacggt         <  1:11440/300‑23 (MQ=255)                                                                         attCATCG‑TTGGGGTCGGTTATAAATTCTGATTAGCCAGGTAACACAGTGTTATGACAGCCCGCCGGAACCGGTGGGCTTTTTTGTGGGGTGAATATGGCAGTAAAGATTTCAGGAGTCCTGAAAGACGGCACAGGAAAACCGGTACANAACTGCACCATTCAGCTGAAAGCCAGNCGTAACAGCACCACGGTGGTGGTGAACA‑CGGTGGGCTCAGAGAATCCGGATGAAGCCGGGCGTTACAGCATGGATGTGGAGTACGGTCAGTACAgtgtcatcctgcaggttgacggttttccac  <  2:505851/299‑30 (MQ=255)                                                                         attCATCG‑TTGGGGTCGGTTATAAATTCTGATTAGCCAGGTAACACAGTGTTATGACAGCCCGCCGGAACCGGTGGGCTTTTTTGTGGGGTGAATATGGCAGTAAAGATTTCAGGAGTCCTGAAAGACGGCACAGGAAAACCGGTACAGAACTGCACCATTCAGCTGAAAGCCAGACGTAACAGCACCACGGTGGTGGTGAACA‑CGGTGGGCTCAGAGAATCCGGATGAAGCCGGGCGTTACAGCATGGATGTGGAGTACGGTCAGTACAgtgtcatcctgcaggttgacggttttccac  <  1:593447/299‑30 (MQ=255)                                                                         attCATCG‑TTGGGGTCGGTTATAAATTCTGATTAGCCAGGTAACACAGTGTTATGACAGCCCGCCGGAACCGGTGGGCTTTTTTGTGGGGTGAATATGGCAGTAAAGATTTCAGGAGTCCTGAAAGACGGCACAGGAAAACCGGTACAGAACTGCACCATTCAGCTGAAAGCCAGACGTAACAGCACCACGGTGGTGGTGAACA‑CGGTGGGCTCAGAGAATCCGGATGAAGCCGGGCGTTACAGCATGGATGTGGAGTACGGTCAGTACAgtgtcatcctgcaggttgacggttttccac  <  2:334210/299‑30 (MQ=255)                                                                         attCATCG‑TTGGGGTCGGTTATAAATTCTGATTAGCCAGGTAACACAGTGTTATGACAGCCCGCCGGAACCGGTGGGCTTTTTTGTGGGGTGAATATGGCAGTAAAGATNTCAGGAGTCCTGAAAGACGGCACAGGAAAACCGGTACAGAACTGCACCATTCAGCTGAAAGCCAGACGTAACAGCACCACGGTGGTGGTGAACA‑CGGTGGGCTCAGAGAATCCGGATGAAGCCGGGCGTTACAGCATGGATGTGGAGTACGGTCAGTACAgtgtcatcctgcaggttgacggttttccac  <  1:548608/299‑30 (MQ=255)                                                                                                  |                                                                                                                                                                                                                                                                                     TAACCCGACCGAATCCGTGGCCATTGATATTGCTTATGAAGGCCCCGGCAGTGGCGACTGGCGCACTGACGGTTTCATCG‑TGGGTGTCGGTTATAAGTTCTGATTAGCCAGGTAACACAGTGTTATGACAGCCCGCCGGTTCAGGCGGGCTTTTTTGTGGGGTGAATATGGCAGTAAAGATTTCAGGTGTACTGAAAGACGGCACAGGAAAACCGGTACAGAACTGCACAATCCAGCTGAAAGCAAAACGTAACAGCACCACGGTGGTGGTGAACA‑CGCTGGCCTCAGAAAATCCGGATGAAGCCGGGCGTTACAGCATGGACGTTGAGTACGGTCAGTACAGCGTTATTCTGTTGGTGGAAGGATTCCCGC  >  NC_000913/1428882‑1429253

Alignment Legend
Aligned base mismatch/match (shaded by quality score): ATCG/ATCG < 3 ≤ ATCG/ATCG < 24 ≤ ATCG/ATCG < 40 ≤ ATCG/ATCG
Unaligned base: atcg    Masked matching base: atcg    Alignment gap: ‑    Deleted base: ‑