Predicted mutation
evidence	seq id	position	mutation	annotation	gene	description
RA	NC_000913	36,231	T→C	intergenic (‑69/+40)	caiD ← / ← caiC	carnitinyl‑CoA dehydratase/putative crotonobetaine/carnitine‑CoA ligase

Read alignment evidence...
	seq id	position		ref	new	freq	score (cons/poly)	reads	annotation	genes	product
*	NC_000913	36,231	0	T	C	95.5%	222.7 / ‑4.0	67	intergenic (‑69/+40)	caiD/caiC	carnitinyl‑CoA dehydratase/putative crotonobetaine/carnitine‑CoA ligase
Reads supporting (aligned to +/- strand):  ref base T (1/2);  new base C (30/34);  total (31/36)
Fisher's exact test for biased strand distribution p-value = 1.00e+00
Kolmogorov-Smirnov test that lower quality scores support variant p-value = 1.00e+00

TGCGGGTCAGATGTAATGATTCACTCATTCCTTTTCTCCATTTTTGCTTTTTCAGGGACGACAACATCCCTGCAAAAAATGCATATTGTTTTAGAGTGTGATTATTAGCTGGCAGGGTAGTTCCCTGCTGTTTCATTTATTTCAGATTCTTTCTAATTATTTTCCCCGAGCAATTACGTGGCAGATCTTTTCT  >  NC_000913/36135‑36327                                                                                                 |                                                                                                 tGCGGGTCAGATGTAATGATTCACTCATTCCTTTTCTCCATTTTTGCTTTTTCAGGGACGACAACATCCCTGCAAAAAATGCATATTGTTTTAGAGcgtg                                                                                               <  1:612764/100‑1 (MQ=255) tGCGGGTCAGATGTAATGATTCACTCATTCCTTTTCTCCATTTTTGCTTTTTCAGGGACGACAACATCCCTGCAAAAAATGCATATTGTTTTAGAGcgtg                                                                                               <  1:417318/100‑1 (MQ=255) tGCGGGTCAGATGTAATGATTCACTCATTCCTTTTCTCCATTTTTGCTTTTTCAGGGACGACAACATCCCTGCAAAAAATGCATATTGTTTTAGAGcgtg                                                                                               <  1:247675/100‑1 (MQ=255)    gggTCAGATGTAATGATTCACTCATTCCTTTTCTCCATTTTTGCTTTTTCAGGGACGACAACATCCCTGCAAAAAATGCATATTGTTTTAGAGCGTGatt                                                                                            <  1:26187/100‑1 (MQ=255)       tCAGATGTAATGATTCACTCATTCCTTTTCTCCATTTTTGCTTTTTCAGGGACGACAACATCCCTGCAAAAAATGCATATTGTTTTAGAGCGTGattatt                                                                                         <  1:931770/100‑1 (MQ=255)        cAGATGTAATGATTCACTCATTCCTTTTCTCCATTTTTGCTTTTTCAGGGACGACAACATCCCTGCAAAAAATGCATATTGTTTTAGAGCGTGAttatta                                                                                        >  1:1097284/1‑100 (MQ=255)          gATGTAATGATTCACTCATTCCTTTTCTCCATTTTTTTTTTTTTTTTTATTTCAACATCCCTGCAAATAATGTTTTTTTTTTTATATTGTGTttttta                                                                                        >  2:338874/1‑98 (MQ=255)           aTGTAATGATTCACTCATTCCTTTTCTCCATTTTTGCTTTTTCAGGGACGACAACATCCCTGCAAAAAATGCATATTGTTTTAGAGCGTGATTATTAGCt                                                                                     <  1:901578/100‑1 (MQ=255)            tGTAATGATTCACTCATTCCTTATCTACATTTTTGCTTTTTCATGGACGACAAAAAAAAAAAAAAAAATGCATATTGTTTTAGAGCGTGATTATTAg                                                                                       <  2:1271486/97‑1 (MQ=255)              tAATGATTCACTCATTCCTTTTCTCCATTTTTTCTTTTTCAGGGACGACAACATCCCTGCAAAAAATGCATATTGTTTTAGAGCGTGATTATTAGCTGGc                                                                                  >  2:792242/1‑100 (MQ=255)                aTGATTCACTCATTCCTTTTCTCCATTTTTGCTTTTTCAGGGACGACAACATCCCTGCAAAAAATGCATATTGTTTTAGAGCGTGATTATTAGCTGGCAg                                                                                <  1:1151143/100‑1 (MQ=255)                 tGATTCACTCATTCCTTTTCTCCATTTTTGCTTTTTCAGGGACGACAACATCCCTGCAAAAAATGCATATTGTTTTAGAGCGTGATTATTAGCTGGCAgg                                                                               >  1:134865/1‑100 (MQ=255)                   aTTCACTCATTCCTTTTCTCCATTTTTGCTTTTTCAGGGACGACAACATCCCTGCAAAAAATGCATATTGTTTTAGAGCGTGATTATTAGCTGGCAGGGt                                                                             <  1:712680/100‑1 (MQ=255)                   aTTCACTCATTCCTTTTCTCCATTTTTGCTTTTTCAGGGACGACAACATCCCTGCAAAAAATGCATATTGTTTTAGAGCGTGATTATTAGCTGGCAGGGt                                                                             <  2:261952/100‑1 (MQ=255)                    ttCACTCATTCCTTTTCTCCATTTTTGCTTTTTCAGGGACGACAACATCCCTGCAAAAAATGCATATTGTTTTAGAGCGTGATTATTAGCTGGCAGGGTa                                                                            >  1:769399/1‑100 (MQ=255)                     tCACTCATTCCTTTTCGCCATATTTCTTTTTGCAGGGACGTCAACATCCCTGCAAAAAATGCATATTGTTTTAGAGCGTGATTATTAGCTGGCAGGGt                                                                             <  2:562344/98‑1 (MQ=255)                           aTTCCTTTTCTCCATTTTTGCTTTTTCAGGGACGACAACATCCCTGCAAAAAATGCATATTGTTTTAGAGCGTGATTATTAGCTGGCAGGGTAGTTCCct                                                                     >  1:1081055/1‑100 (MQ=255)                             tCCTTTTCTCCATTTTTGCTTTTTCAGGGACGACAACATCCCTGCAAAAAATGCATATTGTTTTAGCGCGTGATTATTAGCTGGCAGGGTAGTTCCctgc                                                                   >  1:1446355/1‑100 (MQ=255)                                ttttCTCCATTTTTGCTTTTTCAGGGACGACAACATCCCTGCAAAAAATGCATATTGTTTTAGAGCGTGATTATTAGCTGGCAGGGTAGTTCCCTGCTGt                                                                <  1:584202/100‑1 (MQ=255)                                 tttCTCCATTTTTGCTTTTTCAGGGACGACAACATCCCTGCAAAAAATGCATATTGTTTTAGAGCGTGATTATTAGCTGGCAGGGTAGTTCCCTGCTGtt                                                               <  1:194837/100‑1 (MQ=255)                                    cgccATTTTTGCTTTTTCAGGGACGACAACAACCATAAAAAAAATGCATATTGTTTTAGAGCGTGATTATTAGCTGGCAGGGTAGTTCCCTGCTGTTTCa                                                            <  2:1401226/98‑1 (MQ=255)                                      ccATTTTTGCTTTTTCAGGGACGACAACATCCCTGCAAAAAATGCATATTGTTTTAGAGCGTGATTATTAGCTGGCAGGGTAGTTCCCTGCTGTTTCatt                                                          <  2:1404746/100‑1 (MQ=255)                                       cATTTTTGCTTTTAAAGGGACGACATCGTCCCTGCAAAAAATGCATATTGTTTTAGATTGTGATTATTAGCTGGCAGGGTAGTTCCCTGCTGTTTCattt                                                         <  2:1191429/100‑1 (MQ=255)                                          ttttGCTTTTTCAGGGACGACAACATCCCTGCAATCAATGCATATTGTTTTAGTGCGTGATTATTAGCTGGCATGGTAGTTCCCTGCTGTGTCatttatt                                                      <  2:654571/100‑1 (MQ=255)                                          ttttGCTTTTTCAGGGACGACAACATCCCTGCAAAAAATGCATATTGTTTTAGAGCGTGATTATTAGCTGGCAGGGTAGTTCCCTGCTGTTTCatttatt                                                      <  1:1185158/100‑1 (MQ=255)                                          ttttGCTTTTTCAGGGACGACAACATCCCTGCAAAAAATGCATATTGTTTTAGAGCGTGATTATTAGCTGGCAGGGTAGTTCCCTGCTGTTTCatttatt                                                      <  1:722042/100‑1 (MQ=255)                                               cTTTTTCAGGGACGACAACATCCCTGCAAAAAATGCATATTGTTTTAGAGCGTGATTATTAGCTGGCAGGGTAGTTCCCTGCTGTTTCATTTATTTCAGa                                                 >  2:744862/1‑100 (MQ=255)                                                    tCAGGGACGACAACATCCCTGCAAAAAATGCATATTGTTTTAGAGCGTGATTATTAGCTGGCAGGGTAGTTCCCTGCTGTTTCATTTATTTCAGAttctt                                            >  2:1057519/1‑100 (MQ=255)                                                      aGGGACGACAACATCCCTGCAAAAAATGCATATTGTTTTAGAGTGTGATTATTAGCTGGCAGGGTAGTTCCCTGCTGTTTCATTTATTTCAGAttctttc                                          <  1:837851/100‑1 (MQ=255)                                                      aGGGACGACAACATCCCTGCAAAAAATGCATATTGTTTTAGAGCGTGATTATTAGCTGGCAGGGTAGTTCCCTGCTGTTTCATTTATTTCAGAttctttc                                          <  1:667059/100‑1 (MQ=255)                                                        ggACGACAACATCCCTGCAAAAAATGCATATTGTTTTAGAGCGTGATTATTAGCTGGCAGGGTAGTTCCCTGCTGTTTCATTTATTTCAGATTCTTTCTa                                        <  2:1343972/100‑1 (MQ=255)                                                          acgacAACATCCCTGCAAAAAATGCATATTGTTTTAGAGCGTGATTATTAGCTGGCAGGGTAGTTCCCTGCTGTTTCATTTATTTCAGATTCTTTCTAat                                      <  1:338874/100‑1 (MQ=255)                                                            gacAACATCCCTGCAAAAAATGCATATTGTTTTAGAGCGTGATTATTAGCTGGCAGGGTAGTTCCCTGCTGTTTCATTTATTTCAGATTCTTTCTAatta                                    <  1:770637/100‑1 (MQ=255)                                                            gacAACATCCCGGCAAAAAATGCATATTGTTTTAGGGCGTGATTATTAGCTGGCAGGGTAGTTCCCTGCTGTTTCATTTATTTCAGAttctttct                                         <  2:115991/95‑1 (MQ=255)                                                             acaacaTCCCTGCAAAAAATGCATATTGTTTTAGAGCGTGATTATTAGCTGGCAGGGTAGTTCCCTGCTGTTTCATTTATTTCAGATTCTTTCTAattat                                   >  1:484880/1‑100 (MQ=255)                                                              caacaTCCCTGCAAAAAATACATATTGTTTTAGAGCGTGATTATTAGCTGGCAGGGTAGTTCCCTGCTGTTTCATTTATTTCAGATTCTTTCTAattatt                                  >  2:1235368/1‑100 (MQ=255)                                                                acaTCCCTGCAAAAAATGCATATTGTTTTAGAGCGTGATTATTAGCTGGCAGGGTAGTTCCCTGCTGTTTCATTTATTTCAGATTCTTTCTAATTAtttt                                >  1:1371998/1‑100 (MQ=255)                                                                acaTCCCTGCAAAAAATGCATATTGTTTTAGAGCGTGATTATTAGCTGGCAGGGTAGTTCCCTGCTGTTTCATTTATTTCAGATTCTTTCTAATTAtttt                                >  2:1527301/1‑100 (MQ=255)                                                                acaTCCCTGCAAAAAATGCATATTGTTTTAGAGCGTGATTATTAGCTGGCAGGGTAGTTCCCTGCTGTTTCATTTATTTCAGATTCTTTCTAATTAtttt                                >  2:1440780/1‑100 (MQ=255)                                                                    cccTGCAAAAAATGCATATTGTTTTAGAGCGTGATTATTAGCTGGCAGGGTAGTTCCCTGCTGTTTCATTTATTTCAGATTCTTTCTAATTATTTTcccc                            >  2:136554/1‑100 (MQ=255)                                                                    cccTGCAAAAAATGCATATTGTTTTAGAGCGTGATTATTAGCTGGCAGGGTAGTTCCCTGCTGTTTCATTTATTTCAGATTCTTTCTAATTATTTTcccc                            <  2:1544641/100‑1 (MQ=255)                                                                     ccTGCAAAAAATGCATATTGTTTTAGAGCGTGATTATTAGCTGGCAGGGTAGTTCCCTGCTGTTTCATTTATTTCAGATTCTTTCTAATTATTTTCCCCg                           >  1:1573716/1‑100 (MQ=255)                                                                      cTGCAAAAAATGCATATTGTTTTAGAGCGTGATTATTAGCTGGCAGGGTAGTTCCCTGCTGTTTCATTTATTTCAGATTCTTTCTAATTATTTTCCCCGa                          >  1:140200/1‑100 (MQ=255)                                                                      cTGCAAAAAATGCATATTGTTTTAGAGCGTGATTATTAGCTGGCAGGGTAGTTCCCTGCTGTTTCATTTATTTCAGATTCTTTCTAATTATTTTCCCCGa                          >  2:1445968/1‑100 (MQ=255)                                                                       tGCAAAAAATGCATATTGTTTTAGAGCGTGATTATTAGCTGGCAGGGTAGTTCCCTGCTGTTTCATTTATTTCAGATTCTTTCTAATTATTTTCCCCGAg                         <  2:1097279/100‑1 (MQ=255)                                                                        gCAAAAAATGCATATTGTTTTAGATCGTGATTATTAGCTGGCAGGGTAGTTCCCTGCTGTTTCATTTATTTCAGATTCTTTCTAATTATTTTCCCCGAGc                        <  2:25857/100‑1 (MQ=255)                                                                        gCAAAAAATGCATATTGTTTTAGAGCGTGATTATTAGCTGGCAGGGTAGTTCCCTGCTGTTTCATTTATTTCAGATTCTTTCTAATTATTTTCCCCGAGc                        >  2:1214827/1‑100 (MQ=255)                                                                        gCAAAAAATGCATATTGTTTTAGAGCGTGATTATTAGCTGGCAGGGTAGTTCCCTGCTGTTTCATTTATTTCAGATTCTTTCTAATTATTTTCCCCGAGc                        >  2:136064/1‑100 (MQ=255)                                                                          aaaaaaTGCATATTGTTTTAGAGCGTGATTATTAGCTGGCAGGGTAGTTCCCTGCTGTTTCATTTATTTCAGATTCTTTCTAATTATTTTCCCCGAGCaa                      >  1:213271/1‑100 (MQ=255)                                                                            aaaaTGCATATTGTTTTAGAGCGTGATTATTAGCTGGCAGGGTAGTTCCCTGCTGTTTCATTTATTTCAGATTCTTTCTAATTA‑TTTCCCCGAGCAATTa                   <  2:287107/100‑1 (MQ=255)                                                                             aaaTGCATATTGTTTTAGAGCGTGATTATTAGCTGGCAGGGTAGTTCCCTGCTGTTTCATTTATTTCAGATTCTTTCTAATTATTTTCCCCGAGCAATTa                   <  2:1053688/100‑1 (MQ=255)                                                                                   atatTGTTTTAGAGCGTGATTATTAGCTGGCAGGGTAGTTCCCTGCTGTTTCATTTATTTCAGATTCTTTCTAATTATTTTCCCCGAGCAATTACGTGGc             <  2:134865/100‑1 (MQ=255)                                                                                   atatTGTTTTAGAGCGTGATTATTAGCTGGCAGGGTAGTTCCCTGCTGTTTCATTTATTTCAGATTCTTTCTAATTATTTTCCCCGAGCAATTACGTGGc             <  1:1480091/100‑1 (MQ=255)                                                                                    tatTGTTTTTGAGCGTGATTATTAGCTGGCAGGGTAGTTCCCTGCTGTTTCATTTATTTCAGATTCTTTCTAATTATTTTCCCCGAGCAATTACGTGGCa            <  2:989316/100‑1 (MQ=255)                                                                                    tatTGTTTTAGAGCGTGATTATTAGCTGGCAGGGTAGTTCCCTGCTGTTTCATTTATTTCAGATTCTTTCTAATTATTTTCCCCGAGCAATTACGTGGCa            <  1:902130/100‑1 (MQ=255)                                                                                     atTGTTTTAGAGCGTGATTATTAGCTGGCAGGGTAGTTCCCTGCTGTTTCATTTATTTCAGATTCTTTCTAATTATTTTCCCCGAGCAATTACGTgg              >  2:578667/1‑97 (MQ=255)                                                                                     atTGTTTTAGAGCGTGATTATTAGCTGGCAGGGTAGTTCCCTGCTGTTTCATTTATTTCAGATTCTTTCTAATTATTTTCCCCGAGCAATTACGTGGCAg           >  1:1407768/1‑100 (MQ=255)                                                                                      ttGTTTTAGAGCGTGATTATTAGCTGGCAGGGTAGTTCCCTGCTGTTTCATTTATTTCAGATTCTTTCTAATTATTTTCCCCGAGCAATTACGTGGCAGa          >  1:149001/1‑100 (MQ=255)                                                                                      ttGTTTTAGAGCGTGATTATTAGCTGGCAGGGTAGTTCCCTGCTGTTTCATTTATTTCAGATTCTTTCTAATTATTTTCCCCGAGCAATTACGTGGCAGa          <  1:136064/100‑1 (MQ=255)                                                                                       tGTTTTAGAGCGTGATTATTAGCTGGCAGGGTAGTTCCCTGCTGTTTCATTTATTTCAGATTCTTTCTAATTATTTTCCCCGAGCAATTACGTGGCAGAt         >  1:250867/1‑100 (MQ=255)                                                                                        gTTTTAGAGCGTGATTATTAGCTGGCAGGGTAGTTCCCTGCTGTTTCATTTATTTCAGATTCTTTCTAATTATTTTCCCCGAGCAATTACGTGGCAGATc        <  1:1475165/100‑1 (MQ=255)                                                                                          tttAGAGCGTGATTATTAGCTGGCAGGGTAGTTCCCTGCTGTTTCATTTATTTCAGATTCTTTCTAATTATTTTCCCCGAGCAATTACGTGGCAGATCtt      <  2:1326908/100‑1 (MQ=255)                                                                                            tAGAGCGTGATTATTAGCTGGCAGGGTAGTTCCCTGCTGTTTCATTTATTTCAGATTCTTTCTAATTATTTTCCCCGAGCAATTACGTGGCAGATCtttt    >  2:1524907/1‑100 (MQ=255)                                                                                            tAGAGCGTGATTATTAGCTGGCAGGGTAGTTCCCTGCTGTTTCATTTATTTCAGATTCTTTCTAATTATTTTCCCCGAGCAATTACGTGGCAGATCtttt    >  2:575563/1‑100 (MQ=255)                                                                                             agagCGTGATTATTAGCTGGCAGGGTAGTTCCCTGCTGTTTCATTTATTTCAGATTCTTTCTAATTATTTTCCCCGAGCAATTACGTGGCAGATCTTTTc   <  2:1031320/100‑1 (MQ=255)                                                                                             agagCGTGATTATTAGCTGGCAGGGTAGTTCCCTGCTGTTTCATTTATTTCAGATTCTTTCTAATTATTTTCCCCGAGCAATTACGTGGCAGATCTTTTc   <  1:694047/100‑1 (MQ=255)                                                                                              gagCGTGATTATTAGCTGGCAGGGTAGTTCCCTGCTGTTTCATTTATTTCAGATTCTTTCTAATTATTTTCCCCGAGCAATTACGTGGCAGATCTTTTCt  >  2:1389782/1‑100 (MQ=255)                                                                                              gagCGTGATTATTAGCTGGCAGGGTAGTTCCCTGCTGTTTCATTTATTTCAGATTCTTTCTAATTATTTTCCCCGAGCAATTACGTGGCAGATCTTTTCt  >  2:1226170/1‑100 (MQ=255)                                                                                              gagCGTGATTATTAGCTGGCAGGGTAGTTCCCTGCTGTTTCATTTATTTCAGATTCTTTCTAATTATTTTCCCCGAGCAATTACGTGGCAGATCTTTTCt  >  1:1523200/1‑100 (MQ=255)                                                                                              gagCGTGATTATTAGCTGGCAGGGTAGTTCCCTGCTGTTTCATTTATTTCAGATTCTTTCTAATTATTTTCCCCGAGCAATTACGTGGCAGATCTTTTCt  >  2:696558/1‑100 (MQ=255)                                                                                                 |                                                                                                 TGCGGGTCAGATGTAATGATTCACTCATTCCTTTTCTCCATTTTTGCTTTTTCAGGGACGACAACATCCCTGCAAAAAATGCATATTGTTTTAGAGTGTGATTATTAGCTGGCAGGGTAGTTCCCTGCTGTTTCATTTATTTCAGATTCTTTCTAATTATTTTCCCCGAGCAATTACGTGGCAGATCTTTTCT  >  NC_000913/36135‑36327

Alignment Legend
Aligned base mismatch/match (shaded by quality score): ATCG/ATCG < 3 ≤ ATCG/ATCG < 12 ≤ ATCG/ATCG < 27 ≤ ATCG/ATCG < 37 ≤ ATCG/ATCG < 41 ≤ ATCG/ATCG
Unaligned base: atcg    Masked matching base: atcg    Alignment gap: ‑    Deleted base: ‑