Predicted mutation
evidence	seq id	position	mutation	annotation	gene	description
RA	NC_000913	1,742,575	G→A	intergenic (+14/+26)	cfa → / ← ribC	cyclopropane fatty acyl phospholipid synthase, SAM‑dependent/riboflavin synthase, alpha subunit

Read alignment evidence...
	seq id	position		ref	new	freq	score (cons/poly)	reads	annotation	genes	product
*	NC_000913	1,742,575	0	G	A	100.0%	176.4 / NA	55	intergenic (+14/+26)	cfa/ribC	cyclopropane fatty acyl phospholipid synthase, SAM‑dependent/riboflavin synthase, alpha subunit
Reads supporting (aligned to +/- strand):  ref base G (0/0);  new base A (23/32);  total (23/32)

TAAACGAATGTTTACCTATTATCTGAATGCCTGTGCAGGTGCTTTCCGCGCCCGTGATATTCAGCTCTGGCAGGTCGTGTTCTCACGCGGTGTTGAAAACGGCCTTCGAGTGGCTCGCTAAAGGCTATTCTATCGCCCCCTCTCCGGGGGCGATTTCAGATCAGGCTTCTGTGCCTGGTTGATTCATGGCATTTTCTCGTGCCGCCAGCACACGTTCTACCGTATCTACCACTGCCTGAGTTTGTGGATCGATTTC  >  NC_000913/1742441‑1742696                                                                                                                                       |                                                                                                                          tAAACGAATGTTTACCTATTATCTGAATGCCTGTGCAGGTGCTTTCCGCGCCCGTGATATTCAGCTCTGGCAGGTCGTGTTCTCACGCGGTGTTGAAAACGGCCTTCGAGTGGCTCGCTAAAGGCTATTCTATCAcccc                                                                                                                       <  2:1332080/139‑1 (MQ=255)         tGTTTACCTATTATCTGAATGCCTGTGCAGGTGCTTTCCGCGCCCGTGATATTCAGCTCTGGCAGGTCGTGTTCTCACGCGGTGTTGAAAACGGCCTTCGAGTGGCTCGCTAAAGGCTATTCTATCACCCCCTCTCCgg                                                                                                               >  1:159420/1‑139 (MQ=255)             tACCTATTATCTGAATGCCTGTGCAGGTGCTTTCCGCGCCCGTGATATTCAGCTCTGGCAGGTCGTGTTCTCACGCGGTGTTGAAAACGGCCTTCGAGTGGCTCGCTAAAGGCTATTCTATCACCCCCTCTCCggg                                                                                                              <  1:272611/136‑1 (MQ=255)             tACCTATTATCTGAATGCCTGTGCAGGTGCTTTCCGCGCCCGTGATATTCAGCTCTGGCAGGTCGTGTTCTCACGCGGTGTTGAAAACGGCCTTCGAGTGGCTCGCTAAAGGCTATTCTATCACCCCCTCTCCggg                                                                                                              >  2:272611/1‑136 (MQ=255)                   ttatCTGAATGCCTGTGCAGGTGCTTTCCGCGCCCGTGATATTCAGCTCTGGCAGGTCGTGTTCTCACGCGGTGTTGAAAACGGCCTTCGAGTGGCTCGCTAAAGGCTATTCTATCACCCCCTCTCCGGGGGCGATTTc                                                                                                     >  1:1630242/1‑139 (MQ=255)                      tCTGAATGCCTGTGCAGGTGCTTTCCGCGCCCGTGATATTCAGCTCTGGCAGGTCGTGTTCTCACGCGGTGTTGAAAACGGCCTTCGAGTGGCTCGCTAAAGGCTATTCTATCACCCCCTCTCCGGGGGCGATTTCAGa                                                                                                  >  1:1504372/1‑139 (MQ=255)                         gAATGCCTGTGCAGGTGCTTTCCGCGCCCGTGATATTCAGCTCTGGCAGGTCGTGTTCTCACGCGGTGTTGAAAACGGCCTTCGAGTGGCTCGCTAAAGGCTATTCTATCACCCCCTCTCCGGGGGCGATTTCAGATCa                                                                                               <  1:1188492/139‑1 (MQ=255)                         gAATGCCTGTGCAGGTGCTTTCCGCGCCCGTGATATTCAGCTCTGGCAGGTCGTGTTCTCACGCGGTGTTGAAAACGGCCTTCGAGTGGCTCGCTAAAGGCTATTCTATCACCCCCTCTCCGGGGGCGATTTCAGATCa                                                                                               >  2:844897/1‑139 (MQ=255)                         gAATGCCTGTGCAGGTGCTTTCCGCGCCCGTGATATTCAGCTCTGGCAGGTCGTGTTCTCACGCGGTGTTGAAAACGGCCTTCGAGTGGCTCGCTAAAGGCTATTCTATCACCCCCTCTCCGGGGGCGATTTCAGATCa                                                                                               >  1:1546628/1‑139 (MQ=255)                              ccTGTGCAGGTGCTTTCCGCGCCCGTGATATTCAGCTCTGGCAGGTCGTGTTCTCACGCGGTGTTGAAAACGGCCTTCGAGTGGCTCGCTAAAGGCTATTCTATCACCCCCTCTCCGGGGGCGATTTCAGATCAGGCtt                                                                                          <  1:711064/139‑1 (MQ=255)                              ccTGTGCAGGTGCTTTCCGCGCCCGTGATATTCAGCTCTGGCAGGTCGTGTTCTCACGCGGTGTTGAAAACGGCCTTCGAGTGGCTCGCTAAAGGCTATTCTATCACCCCCTCTCCGGGGGCGATTTCAGATCAGGCtt                                                                                          <  2:1546628/139‑1 (MQ=255)                              ccTGTGCAGGTGCTTTCCGCGCCCGTGATATTCAGCTCTGGCAGGTCGTGTTCTCACGCGGTGTTGAAAACGGCCTTCGAGTGGCTCGCTAAAGGCTATTCTATCACCCCCTCTCCGGGGGCGATTTCAGATCAGGCtt                                                                                          <  2:856543/139‑1 (MQ=255)                                tgtgCAGGTGCTTTCCGCGCCCGTGATATTCAGCTCTGGCAGGTCGTGTTCTCACGCGGTGTTGAAAACGGCCTTCGAGTGGCTCGCTAAAGGCTATTCTATCACCCCCTCTCCggggg                                                                                                            <  2:246394/119‑1 (MQ=255)                                tgtgCAGGTGCTTTCCGCGCCCGTGATATTCAGCTCTGGCAGGTCGTGTTCTCACGCGGTGTTGAAAACGGCCTTCGAGTGGCTCGCTAAAGGCTATTCTATCACCCCCTCTCCggggg                                                                                                            >  1:246394/1‑119 (MQ=255)                                  tgCAGGTGCTTTCCGCGCCCGTGATATTCAGCTCTGGCAGGTCGTGTTCTCACGCGGTGTTGAAAACGGCCTTCGAGTGGCTCGCTAAAGGCTATTCTATCACCCCCTCTCCggggg                                                                                                            >  2:21271/1‑117 (MQ=255)                                  tgCAGGTGCTTTCCGCGCCCGTGATATTCAGCTCTGGCAGGTCGTGTTCTCACGCGGTGTTGAAAACGGCCTTCGAGTGGCTCGCTAAAGGCTATTCTATCACCCCCTCTCCggggg                                                                                                            <  1:21271/117‑1 (MQ=255)                                    cAGGTGCTTTCCGCGCCCGTGATATTCAGCTCTGGCAGGTCGTGTTCTCACGCGGTGTTGAAAACGGCCTTCGAGTGGCTCGCTAAAGGCTATTCTATCACCCCCTCTCCGGGGGCGATTTCAGATCAGGCTTCTGTGc                                                                                    <  2:159420/139‑1 (MQ=255)                                    cAGGTGCTTTCCGCGCCCGTGATATTCAGCTCTGGCAGGTCGTGTTCTCACGCGGTGTTGAAAACGGCCTTCGAGTGGCTCGCTAAAGGCTATTCTATCACCCCCTCTCCGGGGGCGATTTCAGATCAGGCTTCTGTGc                                                                                    <  1:1416636/139‑1 (MQ=255)                                       ttGCTTTCCGCGCCCGTGATTTTCAGCTCTGGCAGGCCGTGTTCTCACGCGGTGTTGAAAACGGCCTTCGAGTGGCGCGCTAAAGGCTATTCTATCACCCCCTCTCCGGGGGCGATTTCAGATCAGGCTTCTGTGCCTg                                                                                 >  1:400577/2‑139 (MQ=255)                                        tGCTTTCCGCGCCCGTGATATTCAGCTCTGGCAGGTCGTGTTCTCACGCGGTGTTGAAAACGGCCTTCGAGTGGCTCGCTAAAGGCTATTCTATCACCCCCTCTCCGGGGGCGATTTCAGATCAGGCTTCTGTGCCTgg                                                                                <  2:1201767/139‑1 (MQ=255)                                                  gcCCGTGATATTCAGCTCTGGCAGGTCGTGTTCTCACGCGGTGTTGAAAACGGCCTTCGAGTGGCTCGCTAAAGGCTATTCTATCAcccc                                                                                                                       <  1:1454930/90‑1 (MQ=255)                                                  gcCCGTGATATTCAGCTCTGGCAGGTCGTGTTCTCACGCGGTGTTGAAAACGGCCTTCGAGTGGCTCGCTAAAGGCTATTCTATCAcccc                                                                                                                       >  2:1454930/1‑90 (MQ=255)                                                   cccGTGATATTCAGCTCTGGCAGGTCGTGTTCTCACGCGGTGTTGAAAACGGCCTTCGAGTGGCTCGCTAAAGGCTATTCTATCACCCCCTCTCCGGGGGCGATTTCAGATCAGGCTTCTGTGc                                                                                    >  2:937433/1‑124 (MQ=255)                                                   cccGTGATATTCAGCTCTGGCAGGTCGTGTTCTCACGCGGTGTTGAAAACGGCCTTCGAGTGGCTCGCTAAAGGCTATTCTATCACCCCCTCTCCGGGGGCGATTTCAGATCAGGCTTCTGTGc                                                                                    <  1:937433/124‑1 (MQ=255)                                                                 ctctGGCAGGTCGTGTTCTCACGCGGTGTTGAAAACGGCCTTCGAGTGGCTCGCTAAAGGCTATTCTATCACCCCCTCTCCGGGGGCGATTTCAGATCAGGCtt                                                                                          >  1:1265563/1‑104 (MQ=255)                                                                 ctctGGCAGGTCGTGTTCTCACGCGGTGTTGAAAACGGCCTTCGAGTGGCTCGCTAAAGGCTATTCTATCACCCCCTCTCCGGGGGCGATTTCAGATCAGGCtt                                                                                          <  2:1265563/104‑1 (MQ=255)                                                                 ctctGGCAGGTCGTGTTCTCACGCGGTGTTGAAAACGGCCTTCGAGTGGCTCGCTAAAGGCTATTCTATCACCCCCTCTCCGGGGGCGATTTCAGATCAGGCTTCTGTGCCTGGTTGATTCATGGCATTTTCTCGTgcc                                                       <  1:531352/139‑1 (MQ=255)                                                                    tGGCAGGTCGTGTTCTCACGCGGTGTTGAAAACGGCCTTCGAGTGGCTCGCTAAAGGCTATTCTATCACCCCCTCTCCGGGGGCGATTTCAGATCAGGCTTCTGTGCCTGGTTGATTCATGGc                                                                    <  2:1665725/123‑1 (MQ=255)                                                                    tGGCAGGTCGTGTTCTCACGCGGTGTTGAAAACGGCCTTCGAGTGGCTCGCTAAAGGCTATTCTATCACCCCCTCTCCGGGGGCGATTTCAGATCAGGCTTCTGTGCCTGGTTGATTCATGGc                                                                    >  1:1665725/1‑123 (MQ=255)                                                                      gCAGGTCGTGTTCTCACGCGGTGTTGAAAACGGCCTTCGAGTGGCTCGCTAAAGGCTATTCTATCACCCCCTCTCCg                                                                                                                >  2:1868894/1‑77 (MQ=255)                                                                      gCAGGTCGTGTTCTCACGCGGTGTTGAAAACGGCCTTCGAGTGGCTCGCTAAAGGCTATTCTATCACCCCCTCTCCg                                                                                                                <  1:1868894/77‑1 (MQ=255)                                                                      gCAGGTCGTGTTCTCACGCGGTGTTGAAAACGGCCTTCGAGTGGCTCGCTAAAGGCTATTCTATCACCCCCTCTCCGGGGGCGATTTCAGATCAGGCTTCTGTGCCTGGTTGATTCATGGCATTTTCTCGTGCCGCCAg                                                  >  1:1522950/1‑139 (MQ=255)                                                                       cAGGTCGTGTTCTCACGCGGTGTTGAAAACGGCCTTCGAG‑GGCTCGCTAAAGGCTATTCTATCACCCCCTCTCCGGGGGCGATTTCAGATCAGGCTTCTGTGCCTGGTTGATTCATGGCATTTTCTCGTGCCGCCAGca                                                <  2:1756400/139‑1 (MQ=255)                                                                         ggTCGTGTTCTCACGCGGTGTTGAAAACGGCCTTCGAGTGGCTCGCTAAAGGCTATTCTATCACCCCCTCTCCGGGGGCGATTTCAGATCAGGCTTCTGTGCCTGGTTGATTCATGGCATTTTCTCGTGCCGCCAGcac                                               <  1:64132/139‑1 (MQ=255)                                                                         ggTCGTGTTCTCACGCGGTGTTGAAAACGGCCTTCGAGTGGCTCGCTAAAGGCTATTCTATCACCCCCTCTCCGGGGGCGATTTCAGATCAGGCTTCTGTGCCTGGTTGATTCATGGCATTTTCTCGTGCCGCCAGcac                                               <  1:844897/139‑1 (MQ=255)                                                                         ggTCGTGTTCTCACGCGGTGTTGAAAACGGCCTTCGAGTGGCTCGCTAAAGGCTATTCTATCACCCCCTCTCCGGGGGCGATTTCAGATCAGGCTTCTGTGCCTGGTTGATTCATGGCATTTTCTCGTGCCGCCAGcac                                               >  2:1818960/1‑139 (MQ=255)                                                                          gTCGTGTTCTCACGCGGTGTTGAAAACGGCCTTCGAGTGGCTCGCTAAAGGCTATTCTATCACCCCCTCTCCGGGGGCGATTTCAGATCAGGCTTCTGTGCCTGGTTGATTCATGGCATTTTCTCGTGCCGCCAGcaca                                              <  2:1504372/139‑1 (MQ=255)                                                                           tCGTGTTCTCACGCGGTGTTGAAAACGGCCTTCGAGTGGCTCGCTAAAGGCTATTCTATCACCCCCTCTCCGGGGGCGATTTCAGATCAGGCTTCTGTGCCTGGTTGATTCATGGCATTTTCTCGTGCCGCCAGCacac                                             >  2:473858/1‑139 (MQ=255)                                                                              tgtTCTCACGCGGTGTTGAAAACGGCCTTCGAGTGGCTCGCTAAAGGCTATTCTATCACCCCCTCTCCGGGGGCGATTTCAGATCAGGCTTCTGTGCCTGGTTGATTCATGGCATTTTCTCGTGCCGCCAGCACACGtt                                          <  2:1630242/139‑1 (MQ=255)                                                                              tgtTCTCACGCGGTGTTGAAAACGGCCTTCGAGTGGCTCGCTAAAGGCTATTCTATCACCCCCTCTCCGGGGGCGATTTCAGATCAGGCTTCTGTGCCTGGTTGATTCATGGCATTTTCTCGTGCCGCCAGCACACGtt                                          <  1:1549174/139‑1 (MQ=255)                                                                              tgtTCTCACGCGGTGTTGAAAACGGCCTTCGAGTGGCTCGCTAAAGGCTATTCTATCACCCCCTCTCCGGGGGCGATTTCAGATCAGGCTTCTGTGCCTGGTTGATTCATGGCATTTTCTCGTGCCGCCAGCACACGtt                                          <  2:1522950/139‑1 (MQ=255)                                                                                ttCTCACGCGGTGTTGAAAACGGCCTTCGAGTGGCTCGCTAAAGGCTATTCTATCACCCCCTCTCCGGGGGCGATTTCAGATCAGGCTTCTGTGCCTGGt                                                                               <  2:1277128/100‑1 (MQ=255)                                                                                ttCTCACGCGGTGTTGAAAACGGCCTTCGAGTGGCTCGCTAAAGGCTATTCTATCACCCCCTCTCCGGGGGCGATTTCAGATCAGGCTTCTGTGCCTGGt                                                                               >  1:1277128/1‑100 (MQ=255)                                                                                 tctcACGCGGTGTTGAAAACGGCCTTCGAGTGGCTCGCTAAAGGCTATTCTATCACCCCCTCTCCGGGGGCGATTTCAGATCAGGCTTCTGTGCCTGGTTGATTCATGGCATTTTCTCGTGCCGCCAGCACACGTTCTa                                       <  1:284754/139‑1 (MQ=255)                                                                                 tctcACGCGGTGTTGAAAACGGCCTTCGAGTGGCTCGCTAAAGGCTATTCTATCACCCCCTCTCCGGGGGCGATTTCAGATCAGGCTTCTGTGCCTGGTTGATTCATGGCATTTTCTCGTGCCGCCAGCACACGTTCTa                                       <  2:372569/139‑1 (MQ=255)                                                                                             ttGAAAACGGCCTTCGAGTGGCTCGCTAAAGGCTATTCTATCACCCCCTCTCCGGGGGCGATTTCAGATCAGGCTTCTGTGCCTGGTTGATTCATGGCATTTTCTCGTGCCGCCAGCACACGTTCTACCGTATCTACCa                           >  1:969875/1‑139 (MQ=255)                                                                                                    cGGCCTTCGAGTGGCTCGCTAAAGGCTATTCTATCACCCCCTCTCCGGGGGCGATTTCAGATCAGGCTTCTGTGCCTGGTTGATTCATGGCATTTTCTCGTGCCGCCAGCACACGTTCTACCGTATCTACCACTGCCTg                    <  1:1818960/139‑1 (MQ=255)                                                                                                     ggCCTTCGAGTGGCTCGCTAAAGGCTATTCTATCACCCCCTCTCCGGGGGCGATTTCAGATCAGGCTTCTGTGCCTGGTTGATTCATGGCATTTTCTCGTGCCGCCAGCACACGTTCTACCGTATCTACCa                           <  2:1266669/131‑1 (MQ=255)                                                                                                     ggCCTTCGAGTGGCTCGCTAAAGGCTATTCTATCACCCCCTCTCCGGGGGCGATTTCAGATCAGGCTTCTGTGCCTGGTTGATTCATGGCATTTTCTCGTGCCGCCAGCACACGTTCTACCGTATCTACCa                           >  1:1266669/1‑131 (MQ=255)                                                                                                                 gCTCGCTAAAGGCTATTCTATCACCCCCTCTCCggggg                                                                                                            <  1:1660399/38‑1 (MQ=255)                                                                                                                 gCTCGCTAAAGGCTATTCTATCACCCCCTCTCCggggg                                                                                                            >  2:1660399/1‑38 (MQ=255)                                                                                                                     gCTAAAGGCTATTCTATCACCCCCTCTCCGGGGGCGATTTCAGCTCAGGCTTCTGTGCCTGGTTGATTCATGGCATTTTCTCGTGCCGCCAGCACACGTTCTACCGTATCTACCACTGCCTGAGTTTGTGGATCGAttt   <  1:473858/139‑1 (MQ=255)                                                                                                                      cTAAAGGCTATTCTATCACCCCCTCTCCGGGGGCGATTTCAGATCAGGCTTCTGTGCCTGGTTGATTCATGGCATTTTCTCGTGCCGCCAGCACACGTTCTACCGTATCTACCACTGCCTGAGTTTGTGGATCGATTTc  >  2:1070579/1‑139 (MQ=255)                                                                                                                       tAAAGGCTATTCTATCACCCCCTCTCCGGGGGCGATTTCAGATCAGGCTTCTGTGCCTGGTTGATTCATGGCATTTTCTCGTGCCGCCAGCACACGTTCTAcc                                     <  2:1528322/103‑1 (MQ=255)                                                                                                                       tAAAGGCTATTCTATCACCCCCTCTCCGGGGGCGATTTCAGATCAGGCTTCTGTGCCTGGTTGATTCATGGCATTTTCTCGTGCCGCCAGCACACGTTCTAcc                                     >  1:1528322/1‑103 (MQ=255)                                                                                                                                       |                                                                                                                          TAAACGAATGTTTACCTATTATCTGAATGCCTGTGCAGGTGCTTTCCGCGCCCGTGATATTCAGCTCTGGCAGGTCGTGTTCTCACGCGGTGTTGAAAACGGCCTTCGAGTGGCTCGCTAAAGGCTATTCTATCGCCCCCTCTCCGGGGGCGATTTCAGATCAGGCTTCTGTGCCTGGTTGATTCATGGCATTTTCTCGTGCCGCCAGCACACGTTCTACCGTATCTACCACTGCCTGAGTTTGTGGATCGATTTC  >  NC_000913/1742441‑1742696

Alignment Legend
Aligned base mismatch/match (shaded by quality score): ATCG/ATCG < 3 ≤ ATCG/ATCG < 27 ≤ ATCG/ATCG < 35 ≤ ATCG/ATCG < 39 ≤ ATCG/ATCG < 40 ≤ ATCG/ATCG
Unaligned base: atcg    Masked matching base: atcg    Alignment gap: ‑    Deleted base: ‑