Predicted mutation
evidence	seq id	position	mutation	annotation	gene	description
RA	NC_000913	3,768,131	A→T	pseudogene (911/945 nt)	rhsJ →	Rhs‑family protein

Read alignment evidence...
	seq id	position		ref	new	freq	score (cons/poly)	reads	annotation	genes	product
*	NC_000913	3,768,131	0	A	T	100.0%	144.1 / NA	41	pseudogene (911/945 nt)	rhsJ	Rhs‑family protein
Reads supporting (aligned to +/- strand):  ref base A (0/0);  new base T (20/21);  total (20/21)

GGAACTAATGGTAAGTTAAAAATGGATACAGTGCTAACAGCACCAACGAACCTTAATTCAAATAAGGATCTAATGGCTATAACAACAAAAGACCTTGGTAATTGGATAACATATGGGCCATCTGGGCACCCCATTTCTAATATGCAAGGTACGCCAGAAAAACCCAGTGATATAAGATAGGTTGTAGATGTATGAAAGCATGCTTGTTACTATTTTTTTATTTCTCTTTTATTTGTCAATTGCATGGTGCTGATGTGAAAATAAAACAAAACGAAAGTAT  >  NC_000913/3767986‑3768265                                                                                                                                                  |                                                                                                                                       ggAACTAATGGTAAGTTAAAAATGGATACAGTGCTAACAGCACCAACGAACCTTAATTCAAATAAGGATCTAATGGCTATAACAACAAAAGACCTTGGTAATTGGATAACATATGGGCCATCTGGGCACCCCATTTCTAATATGCTAgg                                                                                                                                     >  7:113287/1‑149 (MQ=255)                                tGCTAACAGCACCAACGAACCTTAATTCAAATAAGGATCTAATGGCTATAACAACAAAAGACCTTGGTAATTGGATAACATATGGGCCATCTGGGCACCCCATTTCTAATATGCTAg                                                                                                                                      >  4:160306/1‑117 (MQ=255)                                tGCTAACAGCACCAACGAACCTTAATTCAAATAAGGATCTAATGGCTATAACAACAAAAGACCTTGGTAATTGGATAACATATGGGCCATCTGGGCACCCCATTTCTAATATGCTAg                                                                                                                                      <  3:160306/117‑1 (MQ=255)                                  cTAACAGCACCAACGAACCTTAATTCAAATAAGGATCTAATGGCTATAACAACAAAAGACCTTGGTAATTGGATAACATATGGGCCATCTGGTCACCCCATTTCTAATATGCTAGGTACGCCAGAAAAACCCAGTGATATAAGATAGGt                                                                                                    <  7:36052/149‑1 (MQ=255)                                        gCACCAACGAACCTTAATTCAAATAAGGATCTAATGGCTATAACAACAAAAGACCTTGGTAATTGGATAACATATGGGCCATCTGGGCACCCCATTTCTAATATGCTAGGTACGCCAGAAAAACCCAGTGATATAAGATAGGTTGTAGa                                                                                              <  8:113287/149‑1 (MQ=255)                                         cACCAACGAACCTTAATTCAAATAAGGATCTAATGGCTATAACAACAAAAGACCTTGGTAATTGGATAACATATGGGCCATCTGGGCACCCCATTTCTAATATGCTAGGTACGCCAGAAAAACCCAGTGATATAAGATAGGTTGTAGAt                                                                                             <  5:166619/149‑1 (MQ=255)                                                 aaCCTTAATTCAAATAAGGATCTAATGGCTATAACAACAAAAGACCTTGGTAATTGGATAACATATGGGCCATCTGGGCACCCCATTTCTAATATGCTAGGTACGCCAGAAAAACCCAGTGATATAAGATAGGtt                                                                                                   <  8:24222/135‑1 (MQ=255)                                                        aTTCAAATAAGGATCTAATGGCTATAACAACAAAAGACCTTGGTAATTGGATAACATATGGGCCATCTGGGCACCCCATTTCTAATATGCTAGGTACGCCAGAAAAACCCAGt                                                                                                                  <  6:99840/113‑1 (MQ=255)                                                        aTTCAAATAAGGATCTAATGGCTATAACAACAAAAGACCTTGGTAATTGGATAACATATGGGCCATCTGGGCACCCCATTTCTAATATGCTAGGTACGCCAGAAAAACCCAGt                                                                                                                  >  5:99840/1‑113 (MQ=255)                                                         ttCAAATAAGGATCTAATGGCTATAACAACAAAAGACCTTGGTAATTGGATAACATATGGGCCATCTGGGCACCCCATTTCTAATATGCTAGGTACGCCAGa                                                                                                                            >  5:2867/1‑102 (MQ=255)                                                         ttCAAATAAGGATCTAATGGCTATAACAACAAAAGACCTTGGTAATTGGATAACATATGGGCCATCTGGGCACCCCATTTCTAATATGCTAGGTACGCCAGa                                                                                                                            <  6:2867/102‑1 (MQ=255)                                                         ttCAAATAAGGATCTAATGGCTATAACAACAAAAGACCTTGGTAATTGGATAACATATGGGCCATCTGGGCACCCCATTTCTAATATGCTAGGTACGCCAGAAAAACCCAGTGATATAAGATAGGTTGTAGATGTATGAAAGCATGCtt                                                                             >  7:100472/1‑149 (MQ=255)                                                                                 aacaacAAAAGACCTTGGTAATTGGATAACATATGGGCCATCTGGGCACCCCATTTCTAATATGCTAGGTACGCCAGAAAAACCCAGTGATATAAg                                                                                                          >  8:163341/1‑96 (MQ=255)                                                                                 aacaacAAAAGACCTTGGTAATTGGATAACATATGGGCCATCTGGGCACCCCATTTCTAATATGCTAGGTACGCCAGAAAAACCCAGTGATATAAg                                                                                                          <  7:163341/96‑1 (MQ=255)                                                                                  acaacaAAAGACCTTGGTAATTGGATAACATATGGGCCATCTGGGCACCCCATTTCTAATATGCTAGGTACGCCAGAAAAACCCAGTGATATAAGATAGGTTGTAGATGTATGAAAGCATGCTTGTTACTATTTTTTTATTTCTCtttt                                                    <  8:100472/149‑1 (MQ=255)                                                                                   caacaaAAGACCTTGGTAATTGGATAACATATGGGCCATCTGGGCACCCCATTTCTAATATGCTAGGTACGCCAGAAAAACCCAGTGATATAAGATAGGTTGTAGATGTATGAAAGCATGCTTGTTACTATTTTTTTATTTCTCTTTTa                                                   >  1:48229/1‑149 (MQ=255)                                                                                    aacaaAAGACCTTGGTAATTGGATAACATATGGGCCATCTGGGCACCCCATTTCTAATATGCTAGGTACGCCAGAAAAACCCAGTGATATAAGATAGGTTGTAGATGt                                                                                           >  1:26971/1‑108 (MQ=255)                                                                                    aacaaAAGACCTTGGTAATTGGATAACATATGGGCCATCTGGGCACCCCATTTCTAATATGCTAGGTACGCCAGAAAAACCCAGTGATATAAGATAGGTTGTAGATGt                                                                                           <  2:26971/108‑1 (MQ=255)                                                                                    aacaaAAGACCTTGGTAATTGGATAACATATGGGCCATCTGGGCACCCCATTTCTAATATGCTAGGTACGCCAGAAAAACCCAGTGATATAAGATAGGTTGTAGATGTATGaaa                                                                                     <  8:83478/114‑1 (MQ=255)                                                                                    aacaaAAGACCTTGGTAATTGGATAACATATGGGCCATCTGGGCACCCCATTTCTAATATGCTAGGTACGCCAGAAAAACCCAGTGATATAAGATAGGTTGTAGATGTATGaaa                                                                                     >  7:83478/1‑114 (MQ=255)                                                                                      caaAAGACCTTGGTAATTGGATAACATATGGGCCATCTGGGCACCCCATTTCTAATATGCTAGGTACGCCAGAAAAACCCAGTGATATAAGATAGGTTGTAGATGTATGAAAGCATGCTTGTTACTATTTTTTTATTtctc                                                        >  4:40735/1‑141 (MQ=255)                                                                                      caaAAGACCTTGGTAATTGGATAACATATGGGCCATCTGGGCACCCCATTTCTAATATGCTAGGTACGCCAGAAAAACCCAGTGATATAAGATAGGTTGTAGATGTATGAAAGCATGCTTGTTACTATTTTTTTATTtctc                                                        <  3:40735/141‑1 (MQ=255)                                                                                                        ggATAACATATGGGCCATCTGGGCACCCAATTTCTAATATGCTAGGTACGCCAGAAAAACCAAGTGATATAAGATAGGTTGTAGATGTATGAAAGCATGCTTGTTACTATTTTTTTATTTCTCTTTTATTTTTCAATTGCATGGTGCt                               >  8:131567/1‑148 (MQ=255)                                                                                                         gATAACATATGGGCCATCTGGGCACCCCATTTCTAATATGCTAGGTACGCCAGAAAAACCCAGTGATATAAGATAGGTTg                                                                                                  <  7:109696/80‑1 (MQ=255)                                                                                                         gATAACATATGGGCCATCTGGGCACCCCATTTCTAATATGCTAGGTACGCCAGAAAAACCCAGTGATATAAGATAGGTTg                                                                                                  >  8:109696/1‑80 (MQ=255)                                                                                                         gATAACATATGGGCCATCTGGGCACCCCATTTCTAATATGCTAGGTACGCCAGAAAAACCCAGTGATATAAGATAGGTTGTAGATGTATGAAAGCATGCTTGTTACTATTTTTTTATTTCTCTTTTATTTGTCAATTGCATGGTGCTGa                             >  6:22589/1‑149 (MQ=255)                                                                                                             aCATATGGGCCATCTGGGCACCCCATTTCTAATATGCTAGGTACGCCAGAAAAACCCAGTGATATAAGATAGGTTGTAGATGTATGAAAGCATGCTTGTTACTATTTTTTTATTTCTCTTTTATTTGTCAATTGCATGGTGCTGAtgt                          <  5:22589/148‑1 (MQ=255)                                                                                                                tatGGGCCATCTGGGCACCCCATTTCTAATATGCTAGGTACGCCAGAAAAACCCAGTGATATAAGATAGGTTGTAGATg                                                                                            >  5:59501/1‑79 (MQ=255)                                                                                                                tatGGGCCATCTGGGCACCCCATTTCTAATATGCTAGGTACGCCAGAAAAACCCAGTGATATAAGATAGGTTGTAGATg                                                                                            <  6:59501/79‑1 (MQ=255)                                                                                                                 atGGGCCATCTGGGCACCCCATTTCTAATATGCTAGGTACGCCAGAAAAACCCAGTGATATAAGATAGGTTGTAGATGTATGAAAGCATGCTTGTTACTATTTTTTTATTTCTCTTTTATTTGTCAATTGCATGGTGCTGATGTGaaaa                     >  5:61396/1‑149 (MQ=255)                                                                                                                    ggCCATCTGGGCACCCCATTTCTAATATGCTAGGTACGCCAGAAAAACCCAGTGATATAAGATAGGTTGTAGATGTATGAAAGCATGCTTGTTACTATTTTTTTATTTCTCTTTTATTTGTCAATTGCATGGTGCTGATGTGAAAATaa                  <  2:48229/149‑1 (MQ=255)                                                                                                                    ggCCATCTGGGCACCCCATTTCTAATATGCTAGGTACGCCAGAAAAA‑CCAGTGATATAAGATAGGTTGTAGATGTATGAAAGCATGCTTGTTACTAttttt                                                                 <  1:158097/101‑1 (MQ=255)                                                                                                                    ggCCATCTGGGCACCCCATTTCTAATATGCTAGGTACGCCAGAAAAA‑CCAGTGATATAAGATAGGTTGTAGATGTATGAAAGCATGCTTGTTACTAttttt                                                                 >  2:158097/1‑101 (MQ=255)                                                                                                                             ggCACCCCATTTCTAATATGCTAGGTACGCCAGAAAAACCCAGTGATATAAGATAGGTTGTAGATGTATGAAAGCATGCTTGTTACTATTTTTTTATTTCTCTTTTATTTGt                                              >  5:62395/1‑112 (MQ=255)                                                                                                                             ggCACCCCATTTCTAATATGCTAGGTACGCCAGAAAAACCCAGTGATATAAGATAGGTTGTAGATGTATGAAAGCATGCTTGTTACTATTTTTTTATTTCTCTTTTATTTGt                                              <  6:62395/112‑1 (MQ=255)                                                                                                                                  cccATTTCTAATATGCTAGGTACGCCAGAAAAACCCAGTGATATAAGATAGGTTGTAGATGTATGAAAGCATGCTTGTTACTATTTTTTTATTTCTCTTTTATTTGTCAATTGCATGGTGCTGATGTGaaa                      <  7:32/131‑1 (MQ=255)                                                                                                                                  cccATTTCTAATATGCTAGGTACGCCAGAAAAACCCAGTGATATAAGATAGGTTGTAGATGTATGAAAGCATGCTTGTTACTATTTTTTTATTTCTCTTTTATTTGTCAATTGCATGGTGCTGATGTGaaa                      >  8:32/1‑131 (MQ=255)                                                                                                                                  cccATTTCTAATATGCTAGGTACGCCAGAAAAACCCAGTGATATAAGATAGGTTGTAGATGTATGAAAGCATGCTTGTTACTATTTTTTTATTTCTCTTTTATTTGTCAATTGCATGGTGCTGATGTGAAAATaaaa                >  5:85818/1‑137 (MQ=255)                                                                                                                                  cccATTTCTAATATGCTAGGTACGCCAGAAAAACCCAGTGATATAAGATAGGTTGTAGATGTATGAAAGCATGCTTGTTACTATTTTTTTATTTCTCTTTTATTTGTCAATTGCATGGTGCTGATGTGAAAATaaaa                <  6:85818/137‑1 (MQ=255)                                                                                                                                   ccATTTCTAATATGCTAGGTACGCCAGAAAAACCCAGTGATATAAGATAGGTTGTAGATGTATGAAAGCATGCTTGTTACTATTTTTTTATTTCTCTTTTATTTGTCAATTGCATGGTGCTGATGTGAAAATAAAACAAAACGAAAGTa   >  5:122023/1‑149 (MQ=255)                                                                                                                                    cATTTCTAATATGCTAGGTACTCCAGATAAAACTATTTATATAAGATATGTTGTAGATGTATGATAGCATGCTTTTTACTATTTTTTTATTTCTATTTTATTTGTCAATTGCATGGTGCTGATGTGAAAATAAAACAAAACGAAAGTat  <  7:131567/149‑1 (MQ=255)                                                                                                                                                  |                                                                                                                                       GGAACTAATGGTAAGTTAAAAATGGATACAGTGCTAACAGCACCAACGAACCTTAATTCAAATAAGGATCTAATGGCTATAACAACAAAAGACCTTGGTAATTGGATAACATATGGGCCATCTGGGCACCCCATTTCTAATATGCAAGGTACGCCAGAAAAACCCAGTGATATAAGATAGGTTGTAGATGTATGAAAGCATGCTTGTTACTATTTTTTTATTTCTCTTTTATTTGTCAATTGCATGGTGCTGATGTGAAAATAAAACAAAACGAAAGTAT  >  NC_000913/3767986‑3768265

Alignment Legend
Aligned base mismatch/match (shaded by quality score): ATCG/ATCG < 3 ≤ ATCG/ATCG < 14 ≤ ATCG/ATCG < 32 ≤ ATCG/ATCG < 36 ≤ ATCG/ATCG
Unaligned base: atcg    Masked matching base: atcg    Alignment gap: ‑    Deleted base: ‑