Predicted mutation
evidence	seq id	position	mutation	annotation	gene	description
RA	NC_000913	2,775,592	T→C	pseudogene (48/272 nt)	ypjI →	putative UPF0401 protein YpjI

Read alignment evidence...
	seq id	position		ref	new	freq	score (cons/poly)	reads	annotation	genes	product
*	NC_000913	2,775,592	0	T	C	100.0%	128.0 / NA	36	pseudogene (48/272 nt)	ypjI	putative UPF0401 protein YpjI
Reads supporting (aligned to +/- strand):  ref base T (0/0);  new base C (22/14);  total (22/14)

CAGATATATATCATTTCTACAAACATACCCGATTAACGGCAGAATCTCAGGATTCTGCCGCTTTTTTATTATTTTTCAGGGGAGTAGTAATGAGCAACTCTGAAGGTTGGTAGTCATTTTAGCAAACGCTTTCTGGTCTGCCGCAGTGGGCATCGGCTGATTGCGTAGCAGGGCCACTGGTATCTGCCGGTATCACCGACATTAACATTGAAGACGACCAGGGCATTCACGTCCGCCTGATAGTTCGTGATGCCGAAGGTCGGAT  >  NC_000913/2775456‑2775720                                                                                                                                         |                                                                                                                                 cAGATATATATCATTTCTACAAACATACCCGATTAACGGCAGAATCTCAGGATTCTGCCGCTTTTTTATTATTTTTCAGGGGAGTAGTAATGAGCAACTCTGAAGGTTGGTAGTCATTTTAGCAAACGCTTTCTGGCCTg                                                                                                                               <  1:311576/140‑1 (MQ=255)              tttCTACAAACATACCCGATTAACGGCAGAATCTCAGGATTCTGCCGCTTTTTTATTATTTTTCAGGGGAGTAGTAATGAGCAACTCTGAAGGTTGGTAGTCATTTTAGCAAACGCTTTCTGGCCTGCCGCAGTGGGCAt                                                                                                                  >  1:52876/1‑140 (MQ=255)                  tACAAACATACCCGATTAACGGCAGAATCTCAGGATTCTGCCGCTTTTTTATTATTTTTCAGGGGAGTAGTAATGAGCAACTCTGAAGGTTGGTAGTCATTTTAGCAAACGCTTTCTGGCCTGCCGCAGTGGGCATCGGc                                                                                                              >  1:271619/1‑140 (MQ=255)                   aCAAACATACCCGATTAACGGCAGAATCTCAGGATTCTGCCGCTTTTTTATTATTTTTCAGGGGAGTAGTAATGAGCAACTCTGAAGGTTGGTAGTCATTTTAGCAAACGCTTTCTGGCCTGCCGCAGTGGGCATCGGCt                                                                                                             >  1:399531/1‑140 (MQ=255)                         aTACCCGATTAACGGCAGAATCTCAGGATTCTGCCGCTTTTTTATTATTTTTCAGGGGAGTAGTAATGAGCAACTCTGAAGGTTGGTAGTCATTTTAGCAAACGCTTTCTGGCCTGCCGCAGTGGGCATCGGCTGATTGc                                                                                                       >  2:151325/1‑140 (MQ=255)                            cccGATTAACGGCAGAATCTCAGGATTCTGCCGCTTTTTTATTATTTTTCAGGGGAGTAGTAATGAGCAACTCTGAAGGTTGGTAGTCATTTTAGCAAACGCTTTCTGGCCTGCCGCAGTGGGCATCGGCTGATTGCGTa                                                                                                    >  1:495661/1‑140 (MQ=255)                             ccGATTAACGGCAGAATCTCAGGATTCTGCCGCTTTTTTATTATTTTTCAGGGGAGTAGTAATGAGCAACTCTGAAGGTTGGTAGTCATTTTAGCAAACGCTTTCTGGCCTGCCGCAGTGGGCATCGGCTGATTGCGTAg                                                                                                   <  1:419747/140‑1 (MQ=255)                              cGATTAACGGCAGAATCTCAGGATTCTGCCGCTTTTTTATTATTTTTCAGGGGAGTAGTAATGAGCAACTCTGAAGGTTGGTAGTCATTTTAGCAAACGCTTTCTGGCCTGCCGCAGTGGGCATCGGCTGATTGCGTAGc                                                                                                  <  1:379428/140‑1 (MQ=255)                                aTTAACGGCAGAATCTCAGGATTCTGCCGCTTTTTTATTATTTTTCAGGGGAGTAGTAATGAGCAACTCTGAAGGTTGGTAGTCATTTTAGCAAACGCTTTCTGGCCTGCCGCAGTGGGCATCGGCTGATTGCGTAGCAg                                                                                                >  1:703323/1‑140 (MQ=255)                                           aaTCTCAGGATTCTGCCGCTTTTTTATTATTTTTCAGGGGAGTAGTAATGAGCAACTCTGAAGGTTGGTAGTCATTTTAGCAAACGCTTTCTGGCCTGCCGCAGTGGGCATCGGCTGATTGCGTAGCAGGGCCACTGGTa                                                                                     >  2:374089/1‑140 (MQ=255)                                           aaTCTCAGGATTCTGCCGCTTTTTTATTATTTTTCAGGGGAGTAGTAATGAGCAACTCTGAAGGTTGGTAGTCATTTTAGCAAACGCTTTCTGGCCTGCCGCAGTGGGCATCGGCTGATTGCGTAGCAGGGCCACTGGTa                                                                                     <  1:283355/140‑1 (MQ=255)                                              ctcAGGATTCTGCCGCTTTTTTATTATTTTTCAGGGGAGTAGTAATGAGCAACTCTGAAGGTTGGTAGTCATTTTAGCAAACGCTTTCTGGCCTGCCGCAGTGGGCATCGGCTGATTGCGTAGCAGGGCCACTGGTATCt                                                                                  <  2:399531/140‑1 (MQ=255)                                                     ttCTGCCGCTTTTTTATTATTTTTCAGGGGAGTAGTAATGAGCAACTCTGAAGGTTGGTAGTCATTTTAGCAAACGCTTTCTGGCCTGCCGCAGTGGGCATCGGCTGATTGCGTAGCAGGGCCACTGGTATCTGCCGGTa                                                                           >  1:316362/1‑140 (MQ=255)                                                       cTGCCGCTTTTTTATTATTTTTCAGGGGAGTAGTAATGAGCAACTCTGAAGGTTGGTAGTCATTTTAGCAAACGCTTTCTGGCCTGCCGCAGTGGGCATCGGCTGATTGCGTAGCAGGGCCACTGGt                                                                                      <  1:745522/127‑1 (MQ=255)                                                       cTGCCGCTTTTTTATTATTTTTCAGGGGAGTAGTAATGAGCAACTCTGAAGGTTGGTAGTCATTTTAGCAAACGCTTTCTGGCCTGCCGCAGTGGGCATCGGCTGATTGCGTAGCAGGGCCACTGGt                                                                                      >  2:745522/1‑127 (MQ=255)                                                       cTGCCGCTTTTTTATTATTTTTCAGGGGAGTAGTAATGAGCAACTCTGAAGGTTGGTAGTCATTTTAGCAAACGCTTTCTGGCCTGCCGCAGTGGGCATCGGCTGATTGCGTAGCAGGGCCACTGGTATCTGCCGGTATc                                                                         >  2:77131/1‑140 (MQ=255)                                                          ccGCTTTTTTATTATTTTTCAGGGGAGTAGTAATGAGCAACTCTGAAGGTTGGTAGTCATTTTAGCAAACGCTTTCTGGCCTGCCGCAGTGGGCATCGGCTGATTGCGTAGCAGGGCCACTGGTATCTGCCGGTATCAcc                                                                      <  1:374089/140‑1 (MQ=255)                                                              ttttttATTATTTTTCAGGGGAGTAGTAATGAGCAACTCTGAAGGTTGGTAGTCATTTTAGCAAACGCTTTCTGGCCTGCCGCAGTGGGCATCGGCTGATTGCGTAGCAGGGCCACTGGTATCTGCCGGTATCACCGACa                                                                  <  2:495661/140‑1 (MQ=255)                                                                    attattTTTCAGGGGAGTAGTAATGAGCAACTCTGAAGGTTGGTAGTCATTTTAGCAAACGCTTTCTGGCCTGCCGCAGTGGGCATCGGCTGATTGCGTAGCAGGGCCACTGGTATCTGCCGGTATCACCGACATTAACa                                                            <  2:316362/140‑1 (MQ=255)                                                                                   agtagtAATGAGCAACTCTGAAGGTTGGTAGTCATTTTAGCAAACGCTTTCTGGCCTGCCGCAGTGGGCATCGGCTGATTGCGTAGCAGGGCCACTGGTATCTGCCGGTATCACCGACATTAACATTGAAGACGACCAgg                                             <  1:25081/140‑1 (MQ=255)                                                                                     tagtaATGAGCAACTCTGAAGGTTGGTAGTCATTTTAGCAAACGCTTTCTGGCCTGCCGCAGTGGGCATCGGCTGATTGCGTAGCAGGGCCACTGGTATCTGCCGGTATCACCGACATTAACATTGAAGACGACCAGGGc                                           >  2:384292/1‑140 (MQ=255)                                                                                        taATGAGCAACTCTGAAGGTTGGTAGTCATTTTAGCAAACGCTTTCTGGCCTGCCGCAGTGGGCATCGGCTGATTGCGTAGCAGGGCCACTGGCATCTGCCGGTATCACCGACATTAACATTGAAGACGACCAGGGCAtt                                        >  2:631571/1‑140 (MQ=255)                                                                                             aGCAACTCTGAAGGTTGGTAGTCATTTTAGCAAACGCTTTCTGGCCTGCCGCAGTGGGCATCGGCTGATTGCGTAGCAGGGCCACTGGTATCTGCCGGTATCACCGACATTAACATTGAAGACGACCAGGGCATTCACGt                                   >  2:649935/1‑140 (MQ=255)                                                                                             aGCAACTCTGAAGGTTGGTAGTCATTTTAGCAAACGCTTTCTGGCCTGCCGCAGTGGGCATCGGCTGATTGCGTAGCAGGGCCACTGGTATCTGCCGGTATCACCGACATTAACATTGAAGACGACCAGGGCATTCACGt                                   >  1:710882/1‑140 (MQ=255)                                                                                                  ctctGAAGGTTGGTAGTCATTTTAGCAAACGCTTTCTGGCCTGCCGCAGTGGGCATCGGCTGATTGCGTAGCAGGGCCACTGGTATCTGCCGGTATCACCGACATTAACATTGAAGACGACCAGGGCATTCACGTCCGcc                              >  2:81306/1‑140 (MQ=255)                                                                                                     tGAAGGTTGGTAGTCATTTTAGCAAACGCTTTCTGGCCTGCCGCAGTGGGCATCGGCTGATTGCGTAGCAGGGCCACTGGTATCTGCCGGTATCACCGACATTAACATTGAAGACGACCAGGGCATTCACGTCCGCCTGa                           <  2:703323/140‑1 (MQ=255)                                                                                                       aaGGTTGGTAGTCATTTTAGCAAACGCTTTCTGGCCTGCCGCAGTGGGCATCGGCTGATTGCGTAGCAGGGCCACTGGTATCTGCCGGTATCACCGACATTAACATTGAAGACGACCAGGGCATTCACGTCCGCCTGATa                         >  2:412824/1‑140 (MQ=255)                                                                                                            tGGTAGTCATTTTAGCAAACGCTTTCTGGCCTGCCGCAGTGGGCATCGGCTGATTGCGTAGCAGGGCCACTGGTATCTGCCGGTATCACCGACATTAACATTGAAGACGACCAGGGCATTCACGTCCGCCTGATAGTTCg                    >  1:245352/1‑140 (MQ=255)                                                                                                             ggTAGTCATTTTAGCAAACGCTTTCTGGCCTGCCGCAGTGGGCATCGGCTGATTGCGTAGCAGGGCCACTGGTATCTGCCGGTATCACCGACATTAACATTGAAGACGACCAGGGCATTCACGTCCGCCTGATAGTTCGt                   >  2:568732/1‑140 (MQ=255)                                                                                                             ggTAGTCATTTTAGCAAACGCTTTCTGGCCTGCCGCAGTGGGCATCGGCTGATTGCGTAGCAGGGCCACTGGTATCTGCCGGTATCACCGACATTAACATTGAAGACGACCAGGGCATTCACGTCCGCCTGATAGTTCGt                   >  1:122681/1‑140 (MQ=255)                                                                                                                    aTTTTAGCAAACGCTTTCTGGCCTGCCGCAGTGGGCATCGGCTGATTGCGTAGCAGGGCCACTGGTATCTGCCGGTATCACCGACATTAACATTGAAGACGACCAGGGCATTCACGTCCGCCTGATAGTTCGTg                  >  1:68508/1‑134 (MQ=255)                                                                                                                    aTTTTAGCAAACGCTTTCTGGCCTGCCGCAGTGGGCATCGGCTGATTGCGTAGCAGGGCCACTGGTATCTGCCGGTATCACCGACATTAACATTGAAGACGACCAGGGCATTCACGTCCGCCTGATAGTTCGTg                  <  2:68508/134‑1 (MQ=255)                                                                                                                             aaCGCTTTCTGGCCTGCCGCAGTGGGCATCGGCTGATTGCGTAGCAGGGCCACTGGTATCTGCCGGTATCACCGACATTAACATTGAAGACGACCAGGGCATTCACGTCCGCCTGATAGTTCGTGATGCCGAAGGTCGGa   <  1:649935/140‑1 (MQ=255)                                                                                                                             aaCGCTTTCTGGCCTGCCGCAGTGGGCATCGGCTGATTGCGTAGCAGGGCCACTGGTATCTGCCGGTATCACCGACATTAACATTGAAGACGACCAGGGCATTCACGTCCGCCTGATAGTTCGTGATGCCGAAGGTCGGa   <  2:710882/140‑1 (MQ=255)                                                                                                                              aCGCTTTCTGGCCTGCCGCAGTGGGCATCGGCTGATTGCGTAGCAGGGCCACTGGTATCTGCCGGTATCACCGACATTAACATTGAAGACGACCAGGGCATTCACGTCCGCCTGATAGTTCGTGATGCCGAAGGTCGGAt  >  1:415281/1‑140 (MQ=255)                                                                                                                              aCGCTTTCTGGCCTGCCGCAGTGGGCATCGGCTGATTGCGTAGCAGGGCCACTGGTATCTGCCGGTATCACCGACATTAACATTGAAGACGACCAGGGCATTCACGTCCGCCTGATAGTTCGTGATGCCGAAGGTCGGAt  >  1:143117/1‑140 (MQ=255)                                                                                                                                         |                                                                                                                                 CAGATATATATCATTTCTACAAACATACCCGATTAACGGCAGAATCTCAGGATTCTGCCGCTTTTTTATTATTTTTCAGGGGAGTAGTAATGAGCAACTCTGAAGGTTGGTAGTCATTTTAGCAAACGCTTTCTGGTCTGCCGCAGTGGGCATCGGCTGATTGCGTAGCAGGGCCACTGGTATCTGCCGGTATCACCGACATTAACATTGAAGACGACCAGGGCATTCACGTCCGCCTGATAGTTCGTGATGCCGAAGGTCGGAT  >  NC_000913/2775456‑2775720

Alignment Legend
Aligned base mismatch/match (shaded by quality score): ATCG/ATCG < 3 ≤ ATCG/ATCG < 33 ≤ ATCG/ATCG < 34 ≤ ATCG/ATCG < 37 ≤ ATCG/ATCG < 40 ≤ ATCG/ATCG
Unaligned base: atcg    Masked matching base: atcg    Alignment gap: ‑    Deleted base: ‑