Predicted mutation
evidence	seq id	position	mutation	annotation	gene	description
RA	NC_000913	2,210,944	G→A	pseudogene (1845/2001 nt)	yehQ →	pseudogene

Read alignment evidence...
	seq id	position		ref	new	freq	score (cons/poly)	reads	annotation	genes	product
*	NC_000913	2,210,944	0	G	A	100.0%	164.3 / NA	51	pseudogene (1845/2001 nt)	yehQ	pseudogene
Reads supporting (aligned to +/- strand):  ref base G (0/0);  new base A (26/25);  total (26/25)

CGCTACCTTCTGCCAGCGTTTTGCCTGTGCCGTCTACTGCTCATCAGTTGCTGATACGCTGCCAGGCGTTACTTATTCAACTGCTCCATAACGGCTGGCGCTATCAGGAACAGAGTGCTATTGGTCAGGCATAGTTGCTGGCGAATGACCTCACCGCGGTGGGTTTTTATCGGCTGGCACATGTGTTGGGACAATTTCGTAATACAGAAAGCGAGGCACGGGTAGAAGCAATGAATAACGGTGTTTTGCTTTGCGAACAATTA  >  NC_000913/2210811‑2211073                                                                                                                                      |                                                                                                                                  cGCTACCTTCTGCCAGCGTTTTGCCTGTGCCGTCTACTGCTCATCAGTTGCTGATACGCTGCCAGGCGTTACTTATTCAACTGCTCCATAACGGCTGGCGCTATCAGGAACAGAGTGCTATTGGTCAGGCATAATTGCt                                                                                                                              <  2:576809/139‑1 (MQ=255)     aCCTTCTGCCAGCGTTTTGCCTGTGCCGTCTACTGCTCATCAGTTGCTGATACGCTGCCAGGCGTTACTTATTCAACTGCTCCATAACGGCTGGCGCTATCAGGAACAGAGTGCTATTGGTCAGGCATAATTGCTGGCg                                                                                                                          >  2:1171156/1‑139 (MQ=255)         tCTGCCAGCGTTTTGCCTGTGCCGTCTACTGCTCATCAGTTGCTGATACGCTGCCAGGCGTTACTTATTCAACTGCTCCATAACGGCTGGCGCTATCAGGAACAGAGTGCTATTGGTCAGGCATAATTGCTGGCGAATg                                                                                                                      >  2:1533593/1‑139 (MQ=255)                                  cTACTGCTCATCAGTTGCTGATACGCTGCCAGGCGTTACTTATTCAACTGCTCCATAACGGCTGGCGCTATCAGGAACAGAGTGCTATTGGTCAGGCATAATTGCTGGCGAATGACCTCACCGCGGTGGGTTTTTATCg                                                                                             <  1:601890/139‑1 (MQ=255)                                    aCTGCTCATCAGTTGCTGATACGCTGCCAGGCGTTACTTATTCAACTGCTCCATAACGGCTGGCGCTATCAGGAACAGAGTGCTATTGGTCAGGCATAATTGCTGGCGAATGACCTCACCGCGGTGGGTTTTTATCGGc                                                                                           <  2:478200/139‑1 (MQ=255)                                    aCTGCTCATCAGTTGCTGATACGCTGCCAGGCGTTACTTATTCAACTGCTCCATAACGGCTGGCGCTATCAGGAACAGAGTGCTATTGGTCAGGCATAATTGCTGGCGAATGACCTCACCGCGGTGGGTTTTTATCGGc                                                                                           <  1:412242/139‑1 (MQ=255)                                                ttGCTGATACGCTGCCAGGCGTTACTTATTCAACTGCTCCATAACGGCTGGCGCTATCAGGAACAGAGTGCTATTGGTCAGGCATAATTGCTGGCGAATGACCTCACCGCGGTGGGTTTTTATCGGCTGGCACATgtgt                                                                               >  2:1151034/1‑139 (MQ=255)                                                  gCTGATACGCTGCCAGGCGTTACTTATTCAACTGCTCCATAACGGCTGGCGCTATCAGGAACAGAGTGCTATTGGTCAGGCATAATTGCTGGCGAATGACCTCACCGCGGTGGGTTTTTATCGGCTGGCACATGTGTTg                                                                             >  2:782376/1‑139 (MQ=255)                                                             gCCAGGCGTTACTTATTCAACTGCTCCATAACGGCTGGCGCTATCAGGAACAGAGTGCTATTGGTCAGGCATAATTGCTGGCGAATGACCTCACCGCGGTGGGTTTTTATCGGCTGGCACATGTGTTGGGACAATTTCg                                                                  <  1:534037/139‑1 (MQ=255)                                                               cAGGCGTTACTTATTCAACTGCTCCATAACGGCTGGCGCTATCAGGAACAGAGTGCTATTGGTCAGGCATAATTGCTGGCGAATGACCTCACCGCGGTGGGTTTTTATCGGCTGGCACATGTGTTGGGACAATTTCGTa                                                                <  2:430974/139‑1 (MQ=255)                                                                      tACTTATTCAACTGCTCCATAACGGCTGGCGCTATCAGGAACAGAGTGCTATTGGTCAGGCATAATTGCTgg                                                                                                                            <  2:1247720/72‑1 (MQ=255)                                                                      tACTTATTCAACTGCTCCATAACGGCTGGCGCTATCAGGAACAGAGTGCTATTGGTCAGGCATAATTGCTgg                                                                                                                            >  1:1247720/1‑72 (MQ=255)                                                                          tATTCAACTGCTCCATAACGGCTGGCGCTATCAGGAACAGAGTGCTATTGGTCAGGCATAATTGCTGGCGAATGACCTCACCGCGGTGGGTTTTTATCGGCTGGCACATGTGTTGGGACAATTTCGTAATACAGAAAGc                                                     <  1:1171156/139‑1 (MQ=255)                                                                                aCTGCTCCATAACGGCTGGCGCTATCAGGAACAGAGTGCTATTGGTCAGGCATAATTGCTGGCGAATGACCTCACCGCGGTGGGTTTTTATCGGCTGGCACATGTGTTGGGACAATTTCGTAATACAGAAAGCGAGGCa                                               >  1:984720/1‑139 (MQ=255)                                                                                  tGCTCCATAACGGCTGGCGCTATCAGGAACAGAGTGCTATTGGTCAGGCATAATTGCTGGCGAATGACCTCACCGCGGTGGGTTTTTATCGGCTGGCACATGTGTTGGGACAATTTCGTAATACAGAAAGCGAGGCACg                                             >  1:1492058/1‑139 (MQ=255)                                                                                         tAACGGCTGGCGCTATCAGGAACAGAGTGCTATTGGTCAGGCATAATTGCTGGCGAATGACCTCACCGCGGTGGGTTTTTATCGGCTGGcaca                                                                                    <  1:780420/93‑1 (MQ=255)                                                                                         tAACGGCTGGCGCTATCAGGAACAGAGTGCTATTGGTCAGGCATAATTGCTGGCGAATGACCTCACCGCGGTGGGTTTTTATCGGCTGGcaca                                                                                    >  2:780420/1‑93 (MQ=255)                                                                                              gCTGGCGCTATCAGGAACAGAGTGCTATTGGTCAGGCATAATTGCt                                                                                                                              >  2:898673/1‑46 (MQ=255)                                                                                              gCTGGCGCTATCAGGAACAGAGTGCTATTGGTCAGGCATAATTGCt                                                                                                                              <  1:898673/46‑1 (MQ=255)                                                                                              gCTGGCGCTATCAGGAACAGAGTGCTATTGGTCAGGCATAATTGCTGGCGAATGACCTCACCGCGGTGGGTTTTTATCGGCTGGCACATGTGTTGGGACaa                                                                       >  2:1008469/1‑101 (MQ=255)                                                                                              gCTGGCGCTATCAGGAACAGAGTGCTATTGGTCAGGCATAATTGCTGGCGAATGACCTCACCGCGGTGGGTTTTTATCGGCTGGCACATGTGTTGGGACaa                                                                       <  1:1008469/101‑1 (MQ=255)                                                                                               cTGGCGCTATCAGGAACAGAGTGCTATTGGTCAGGCATAATTGCTGGCGAATGACCTCACCGCGGTGGGTTTTTATCGGCt                                                                                          <  1:1272817/81‑1 (MQ=255)                                                                                               cTGGCGCTATCAGGAACAGAGTGCTATTGGTCAGGCATAATTGCTGGCGAATGACCTCACCGCGGTGGGTTTTTATCGGCt                                                                                          >  2:1272817/1‑81 (MQ=255)                                                                                                 ggCGCTATCAGGAACAGAGTGCTATTGGTCAGGCATAATTGCTGGCGAAt                                                                                                                       <  2:808746/50‑1 (MQ=255)                                                                                                 ggCGCTATCAGGAACAGAGTGCTATTGGTCAGGCATAATTGCTGGCGAAt                                                                                                                       >  1:808746/1‑50 (MQ=255)                                                                                                 ggCGCTATCAGGAACAGAGTGCTATTGGTCAGGCATAATTGCTGGCGAATGACCTCACCGCGGTGGGTTTTTATCGGCTGGCACATGTGTTGGGACAATTTCGTAATACAGAAAGCGAGGCACGGGTAGAAGCAATGaa                              >  2:1039565/1‑139 (MQ=255)                                                                                                   cgcTATCAGGAACAGAGTGCTATTGGTCAGGCATAATTGCTGGCGaa                                                                                                                        >  2:374611/1‑47 (MQ=255)                                                                                                   cgcTATCAGGAACAGAGTGCTATTGGTCAGGCATAATTGCTGGCGaa                                                                                                                        <  1:374611/47‑1 (MQ=255)                                                                                                     cTATCAGGAACAGAGTGCTATAGGTCAGGCATAATTGCTGGCGAATGACCTCACCGCGGTGGGTTTTTAACGGCTGGCACATGTGTTGGGACAATTTCGTAATACAGAAAGCGAGGCACGGGTAGAAGCAATGAGTAAc                          <  2:984720/139‑1 (MQ=255)                                                                                                                  agTGCTATTGGTCAGGCATAATTGCTGGCGAATGACCTCACCGCGGTGGGTTTTTATCGGCTgg                                                                                        <  2:753349/64‑1 (MQ=255)                                                                                                                  agTGCTATTGGTCAGGCATAATTGCTGGCGAATGACCTCACCGCGGTGGGTTTTTATCGGCTgg                                                                                        >  1:753349/1‑64 (MQ=255)                                                                                                                  agTGCTATTGGTCAGGCATAATTGCTGGCGAATGACCTCACCGCGGTGGGTTTTTATCGGCTGGCACATGTGTTGGGACAATTTCGTAATACAGAAAGCGAGGc                                                >  2:1136944/1‑104 (MQ=255)                                                                                                                  agTGCTATTGGTCAGGCATAATTGCTGGCGAATGACCTCACCGCGGTGGGTTTTTATCGGCTGGCACATGTGTTGGGACAATTTCGTAATACAGAAAGCGAGGc                                                <  1:1136944/104‑1 (MQ=255)                                                                                                                  agTGCTATTGGTCAGGCATAATTGCTGGCGAATGACCTCACCGCGGTGGGTTTTTATCGGCTGGCACATGTGTTGGGACAATTTCGTAATACAGAAAGCGAGGCACGGGTAGAAGCAATGaa                              <  2:1170005/122‑1 (MQ=255)                                                                                                                  agTGCTATTGGTCAGGCATAATTGCTGGCGAATGACCTCACCGCGGTGGGTTTTTATCGGCTGGCACATGTGTTGGGACAATTTCGTAATACAGAAAGCGAGGCACGGGTAGAAGCAATGaa                              >  1:1170005/1‑122 (MQ=255)                                                                                                                  agTGCTATTGGTCAGGCATAATTGCTGGCGAATGACCTCACCGCGGTGGGTTTTTATCGGCTGGCACATGTGTTGGGACAATTTCGTAATACAGAAAGCGAGGCACGGGTAGAAGCAATGAATAACGGTGTtttgcttt             >  1:881479/1‑139 (MQ=255)                                                                                                                  agTGCTATTGGTCAGGCATAATTGCTGGCGAATGACCTCACCGCGGTGGGTTTTTATCGGCTGGCACATGTGTTGGGACAATTTCGTAATACAGAAAGCGAGGCACGGGTAGAAGCAATGAATAACGGTGTtttgcttt             >  2:626288/1‑139 (MQ=255)                                                                                                                    tGCTATTGGTCAGGCATAATTGCTGGCGAATGACCTCACCGCGGTGGGTTTTTa                                                                                                <  1:802989/54‑1 (MQ=255)                                                                                                                    tGCTATTGGTCAGGCATAATTGCTGGCGAATGACCTCACCGCGGTGGGTTTTTa                                                                                                >  2:802989/1‑54 (MQ=255)                                                                                                                       tATTGGTCAGGCATAATTGCTGGCGAATGACCTCACCGCGGTGGGTTTTTATCGGCTGGCACATGTGTTGGGACaa                                                                       >  1:231514/1‑76 (MQ=255)                                                                                                                       tATTGGTCAGGCATAATTGCTGGCGAATGACCTCACCGCGGTGGGTTTTTATCGGCTGGCACATGTGTTGGGACaa                                                                       <  2:231514/76‑1 (MQ=255)                                                                                                                       tATTGGTCAGGCATAATTGCTGGCGAATGACCTCACCGCGGTGGGTTTTTATCGGCTGGCACATGTGTTGGGACAATTTCGTAATACAGAAAGCGAGGCACGGGTAGAAGCAATGAATAACGGTGTTTTGCTTTGCGaa        <  2:1492058/139‑1 (MQ=255)                                                                                                                         ttGGTCAGGCATAATTGCTGGCGAATGACCTCACCGCGGTGGGTTTTTATCGGCTGGCACATGTGTTGGGACAATTTCGTAATACAGAAAGCGAGGCACGGGTAGAAGCAATGAATAACGGTGTTTTGCTTTGCGAACa      >  1:61662/1‑139 (MQ=255)                                                                                                                            gTCAGGCATAATTGCTGGCGAATGACCTCACCGCGGTGGGTTTTTATCGGCTGGCACATGTGTTGGGACAATTTCGTAATACAGAAAGCGAGGCACGGGTAGAAGCAATGAATAACGGTGTTTTGCTTTGCGAACAatt   >  1:363434/1‑139 (MQ=255)                                                                                                                             tCAGGCATAATTGCTGGCGAATGACCTCACCGCGGTGGGTTTTTATCGGCTGGCACATGTGTTGGGACAATTTCGTAATACAGAAAGCGAGGCACGGGTAGAAGCAATGAATAACGGTGTTTTGCTTTGCGAACAatta  <  1:1533593/139‑1 (MQ=255)                                                                                                                                 gCATAATTGCTGGCGAATGACCTCACCGCGGTGGGTTTTTATCgg                                                                                            <  2:565979/45‑1 (MQ=255)                                                                                                                                 gCATAATTGCTGGCGAATGACCTCACCGCGGTGGGTTTTTATCgg                                                                                            >  1:565979/1‑45 (MQ=255)                                                                                                                                 gCATAATTGCTGGCGAATGACCTCACCGCGGTGGGTTTTTATCGGc                                                                                           <  2:630753/46‑1 (MQ=255)                                                                                                                                 gCATAATTGCTGGCGAATGACCTCACCGCGGTGGGTTTTTATCGGc                                                                                           >  1:630753/1‑46 (MQ=255)                                                                                                                                 gCATAATTGCTGGCGAATGACCTCACCGCGGTGGGTTTTTATCGGCTGGc                                                                                       >  1:829/1‑50 (MQ=255)                                                                                                                                 gCATAATTGCTGGCGAATGACCTCACCGCGGTGGGTTTTTATCGGCTGGc                                                                                       <  2:829/50‑1 (MQ=255)                                                                                                                                      |                                                                                                                                  CGCTACCTTCTGCCAGCGTTTTGCCTGTGCCGTCTACTGCTCATCAGTTGCTGATACGCTGCCAGGCGTTACTTATTCAACTGCTCCATAACGGCTGGCGCTATCAGGAACAGAGTGCTATTGGTCAGGCATAGTTGCTGGCGAATGACCTCACCGCGGTGGGTTTTTATCGGCTGGCACATGTGTTGGGACAATTTCGTAATACAGAAAGCGAGGCACGGGTAGAAGCAATGAATAACGGTGTTTTGCTTTGCGAACAATTA  >  NC_000913/2210811‑2211073

Alignment Legend
Aligned base mismatch/match (shaded by quality score): ATCG/ATCG < 3 ≤ ATCG/ATCG < 30 ≤ ATCG/ATCG < 36 ≤ ATCG/ATCG < 39 ≤ ATCG/ATCG < 40 ≤ ATCG/ATCG
Unaligned base: atcg    Masked matching base: atcg    Alignment gap: ‑    Deleted base: ‑