Predicted mutation
evidence	seq id	position	mutation	annotation	gene	description
RA	NC_000913	4,340,287	G→A	L79F (CTT→TTT)	adiA ←	arginine decarboxylase

Read alignment evidence...
	seq id	position		ref	new	freq	score (cons/poly)	reads	annotation	genes	product
*	NC_000913	4,340,287	0	G	A	98.4%	207.0 / ‑4.1	63	L79F (CTT→TTT)	adiA	arginine decarboxylase
Reads supporting (aligned to +/- strand):  ref base G (0/1);  new base A (23/39);  total (23/40)
Fisher's exact test for biased strand distribution p-value = 1.00e+00
Kolmogorov-Smirnov test that lower quality scores support variant p-value = 8.31e-01

TCGACAAGCTCCAGCAGGTCGCGATCCATTGCGGCGAGGGCTTTTTCCCGATCGCCCAACAGGAAGACCGGCACGTTTTGTTGGCGCTCATGAAGCTTACCGATCAATTGTCTGACGTTTTGATGTTCGTCCGGATGTTCCATTTGATAGCTGAACATCAGGCAGTCAATGGCTTCGTTTGAAGAGAG  >  NC_000913/4340193‑4340380                                                                                               |                                                                                              tCGACAAGCTCCAGCAGGTCGCGATCCATTGCGGCGAGGGCTTTTTCCCGATCGCCCAACAGGAAGACCGGCACGTTTTGTTGGCGCTCATGAAACTTAc                                                                                          <  1:819907/100‑1 (MQ=255)  cGACAAGCTCCAGCAGGTCGCGATCCATTGCGGCGAGGGCTTTTTCCCGATCGCCCAACAGGAAGACCGGCACGTTTTGTTGGCGCTCATGAAACTTAcc                                                                                         <  2:747054/100‑1 (MQ=255)  cGAAAAGCTCCAGCAGGTCGCGATCCATTGCGGCGAGGGCTTTTTCCCGATCGCCCAACAGGAAGACCGGCACGTTTTGTTGGCGCTCATGAAACTTAcc                                                                                         <  2:437953/100‑1 (MQ=255)   gACAAGCTCCAGCAGGTCGCGATCCATTGCGGCGAGGGCTTTTTCCCGATCGCCCAACAGGAAGACCGGCACGTTTTGTTGGCGCTCATGAAACTTACCg                                                                                        <  2:1524683/100‑1 (MQ=255)   gACAAGCTCCAGCAGGTCGCGATCCATTGCGGCGAGGGCTTTTTCCCGATCGCCCAACAGGAAGACCGGCACGTTTTGTTGGCGCTCATGAAACTTACCg                                                                                        >  1:495995/1‑100 (MQ=255)      aaGCTCCAGCAGGTCGCGATCCATTGCGGCGAGGGCTTTTTCCCGATCGCCCAACAGGAAGACCGGCACGTTTTGTTGGCGCTCATGAAACTTACCGATc                                                                                     <  1:489672/100‑1 (MQ=255)       aGCTCCAGCAGGTCGCGATCCATTGCGGCGAGGGCTTTTTCCCGATCGCCCAACAGGAAGACCGGCACGTTTTGTTGGCGCTCATGAAACTTACCGATCa                                                                                    <  2:289869/100‑1 (MQ=255)        gCTCCAGCAGGTCGCGATCCATTGCGGCGAGGGCTTTTTCCCGATCGCCCAACAGGAAGACCGGCACGTTTTGTTGGCGCTCATGAAACTTACCGATCaa                                                                                   >  2:557421/1‑100 (MQ=255)          tCCAGCAGGTCGCGATCCATTGCGGCGAGGGCTTTTTCCCGATCGCCCAACAGGAAGACCGGCACGTTTTGTTGGCGCTCATGAAACTTACCGATCAAtt                                                                                 >  1:950288/1‑100 (MQ=255)             agcagGTCGCGATCCATTGCGGCGAGGGCTTTTTCCCGATCGCCCAACAGGAAGACCGGCACGTTTTGTTGGCGCTCATGAAACTTACCGATCAATTGTc                                                                              <  2:399612/100‑1 (MQ=255)             agcagGTCGCGATCCATTGCGGCGAGGGCTTTTTCCCGATCGCCCAACAGGAAGACCGGCACGTTTTGTTGGCGCTCATGAAACTTACCGATCAATTGTc                                                                              >  1:748884/1‑100 (MQ=255)             agcagGTCGCGATCCATTGCGGCGAGGGCTTTTTCCCGATCGCCCAACAGGAAGACCGGCACGTTTTGTTGGCGCTCATGAAACTTACCGATCAATTGTc                                                                              <  1:716666/100‑1 (MQ=255)             agcagGTCGCGATCCATTGCGGCGAGGGCTTTTTCCCGATCGCCCAACAGGAAGACCGGCACGTTTTGTTGGCGCTCATGAAACTTACCGATCAATTGTc                                                                              >  1:1269949/1‑100 (MQ=255)                 ggTCGCGATCCATTGCGGCGAGGGCTTTTTCCCGATCGCCCAACAGGAAGACCGGCACGTTTTGTTGGCGCTCATGAAACTTACCGATCAATTGTCTGAc                                                                          <  1:158969/100‑1 (MQ=255)                 ggTCGCGATCCATTGCGGCGAGGGCTTTTTCCCGATCGCCCAACAGGAAGACCGGCACGTTTTGTTGGCGCTCATGAAACTTACCGATCAATTGTCTGAc                                                                          <  1:1080773/100‑1 (MQ=255)                 ggTCGCGATCCATTGCGGCGAGGGCTTTTTCCCGATCGCCCAACAGGAAGACCGGCACGTTTTGTTGGCGCTCATGAAACTTACCGATCAATTGTCTGAc                                                                          >  2:544871/1‑100 (MQ=255)                     gcgATCCATTGCGGCGAGGGCTTTTTCCCGATCGCCCAACAGGAAGACCGGCACGTTTTGTTGGCGCTCATGAAACTTACCGATCAATTGTCTGACGttt                                                                      <  2:274236/100‑1 (MQ=255)                      cgATCCATTGCGGCGAGGGCTTTTTCCCGATCGCCCAACAGGAAGACCGGCACGTTTTGTTGGCGCTCATGAAACTTGCCGATCAATTGTCTGACGtttt                                                                     <  2:1320353/100‑1 (MQ=255)                      cgATCCATTGCGGCGAGGGCTTTTTCCCGATCGCCCAACAGGAAGACCGGCACGTTTTGTTGGCGCTCATGAAACTTACCGATCAATTGTCTGACGtttt                                                                     <  1:1496019/100‑1 (MQ=255)                       gATCCATTGCGGCGAGGGCTTTTTCCCGATCGCCCAACAGGAAGACCGGCACGTTTTGTTGGCGCTCATGAAACTTACCGATCAATTGTCTGACGTTTTg                                                                    >  2:822158/1‑100 (MQ=255)                        aTCCATTGCGGCGAGGGCTTTTTCCCGATCGCCCAACAGGAAGACCGGCACGTTTTGTTGGCGCTCATGAAACTTACCGATCAATTGTCTGACGTTTTGa                                                                   <  1:145163/100‑1 (MQ=255)                        aTCCATTGCGGCGAGGGCTTTTTCCCGATCGCCCAACAGGAAGACCGGCACGTTTTGTTGGCGCTCATGAAACTTACCGATCAATTGTCTGACGTTTTGa                                                                   <  1:315402/100‑1 (MQ=255)                          ccATTGCGGCGAGGGCTTTTTCCCGATCGCCCAACAGGAAGACCGGCACGTTTTGTTGGCGCTCATGAAACTTACCGATCAATTGTCTGACGTTTTGATg                                                                 <  2:726510/100‑1 (MQ=255)                           cATTGCGGCGAGGGCTTTTTCCCGATCGCCCAACAGGAAGACCGGCACGTTTTGTTGGCGCTCATGAAACTTACCGATCAATTGTCTGACGTTTTGATGt                                                                >  2:1394833/1‑100 (MQ=255)                            aTTGCGGCGAGGGCTTTTTCCCGATCGCCCAACAGGAAGACCGGCACGTTTTGTTGGCGCTCATGAAACTTACCGATCAATTGTCTGACGTTTTGATGtt                                                               <  1:981187/100‑1 (MQ=255)                            aTTGCGGCGAGGGCTTTTTCCCGATCGCCCAACAGGAAGACCGGCACGTTTTGTTGGCGCTCATGAAACTTACCGATCAATTGTCTGACGTTTTGATGtt                                                               <  2:1106451/100‑1 (MQ=255)                             ttGCGGCGAGGGCTTTTTCCCGATCGCCCAACAGGAAGACCGGCACGTTTTGTTGGCGCTCATGAAACTTACCGATCAATTGTCTGACGTTTTGATGTTc                                                              <  1:603138/100‑1 (MQ=255)                              tGCGGCGAGGGCTTTTTCCCGATCGCCCAACAGGAAGACCGGCACGTTTTGTTGGCGCTCATACAACTTACCGATCCATTGTCTGACGTTTTGATGtt                                                               >  2:1402554/1‑98 (MQ=255)                               gcggcgAGGGCTTTTTCCCGATCGCCCAACAGGAAGACCGGCACGTTTTGTTGGCGCTCATGAAACTTACCGATCAATTGTCTGACGTTTTGATGTTc                                                              >  2:1427569/1‑98 (MQ=255)                                  gcgAGGGCTTTTTCCCGATCGCCCAACAGGAAGACCGGCACGTTTTGTTGGCGCTCATGAAACTTACCGATCAATTGTCTGACGTTTTGATGTTCGTCCg                                                         <  2:819093/100‑1 (MQ=255)                                  gcgAGGGCTTTTTCCCGATCGCCCAACAGGAAGACCGGCACGTTTTGTTGGCGCTCATGAAACTTACCGATCAATTGTCTGACGTTTTGATGTTCGTCCg                                                         <  1:193925/100‑1 (MQ=255)                                      cgccTTTTTCCCTATCGCCCAACAAGAACACCGGCACGTTTTCTTGGCGCTCATGAAACTTACCGATCAATTGTCTGACGTTTTGATGTTCGTCCgg                                                        <  2:1245816/94‑1 (MQ=255)                                       ggCTTTTTCCCGATCGCCCAACAGGAAGACCGGCACGTTTTGTTGGCGCTCATGAAACTTACCGATCAATTGTCTGACGTTTTGATGTTCGTCCGGATGt                                                    >  1:895180/1‑100 (MQ=255)                                         cTTTTTCCCGATCGCCCAACAGGAAGACCGGCACGTTTTGTTGGCGCTCATGAAACTTACCGATCAATTGTCTGACGTTTTGATGTTCGTCCGGATGTTc                                                  >  2:3510/1‑100 (MQ=255)                                               cccGATCGCCCAACAGGAAGACCGGCACGTTTTGTTGTCGCTCATGAAACTTACCGATCAATTGTCTGACGTTTTGATGTTCGTCCGGATGTTCCATTTg                                            >  2:841380/1‑100 (MQ=255)                                                  gATCGCCCAACAGGAAGACCGGCACGTTTTGTTGGCGCTCATGAAACTTACCGATCAATTGTCTGACGTTTTGATGTTCGTCCGGATGTTCCATTTGATa                                         <  1:1179458/100‑1 (MQ=255)                                                   aTCGCCCAACAGGAAGACCGGCACGTTTTGTTGGCGCTCATGAAACTTACCGATCAATTGTCTGACGTTTTGATGTTCGTCCGGATGTTCCATTTGATAg                                        <  1:1053177/100‑1 (MQ=255)                                                      gCCCAACAGGAAGACCGGCACGTTTTGTTGGCGCTCATGAAACTTACCGATCAATTGTCTGACGTTTTGATGTTCGTCCGGATGTTCCATTTGATAGCTg                                     >  1:246139/1‑100 (MQ=255)                                                       cccAACAGGAAGACCGGCACGTTTTGTTGGCGCTCATGAAACTTACCGATCAATTGTCTGACGTTTTGATGTTCGTCCGGATGTTCCATTTGATAGCTGa                                    <  2:449133/100‑1 (MQ=255)                                                         cAACAGGAAGACCGGCACGTTTTGTTGGCGCTCATGAAGCTTACCGATCAATTGTCTGACGTTTTGATGTTCGTCCGGATGTTCCATTTGATAGCTGAAc                                  <  1:1233771/100‑1 (MQ=255)                                                         cAACAGGAAGACCGGCACGTTTTGTTGGCGCTCATGAAACTTACCGATCAATTGTCTGACGTTTTGATGTTCGTCCGGATGTTCCATTTGATAGCTGAAc                                  <  1:1257588/100‑1 (MQ=255)                                                         cAACAGGAAGACCGGCACGTTTTGTTGGCGCTCATGAAACTTACCGATCAATTGTCTGACGTTTTGATGTTCGTCCGGATGTTCCATTTGATAGCTGAAc                                  >  2:457111/1‑100 (MQ=255)                                                          aaCAGGAAGACCGGCACGTTTTGTTGGCGCTCATGAAACTTACCGATCAATTGTCTGACGTTTTGATGTTCGTCCGGATGTTCCATTTGATAGCTGAACa                                 <  1:1244226/100‑1 (MQ=255)                                                             aGGAAGACCGGCACGTTTTGTTGGCGCTCATGAAACTTACCGATCAATTGTCTGACGTTTTGATGTTCGTCCGGATGTTCCATTTGATAGCTGAACATCa                              <  1:963228/100‑1 (MQ=255)                                                              ggAAGACCGGCACGTTTTGTTGGCGCTCATGAAACTTACCGATCAATTGTCTGACGTTTTGATGTTCGTCCGGATGTTCCATTTGATAGCTGAACATCAg                             >  1:500932/1‑100 (MQ=255)                                                              ggAAGACCGGCACGTTTTGTTGGCGCTCATGAAACTTACCGATCAATTGTCTGACGTTTTGATGTTCGTCCGGATGTTCCATTTGATAGCTGAACATCAg                             >  1:686044/1‑100 (MQ=255)                                                              ggAAGACCGGCACGTTTTGTTGGCGCTCATGAAACTTACCGATCAATTGTCTGACGTTTTGATGTTCGTCCGGATGTTCCATTTGATAGCTGAACATCAg                             >  2:749153/1‑100 (MQ=255)                                                                aaGACCGGCACGTTTTGTTGGCGCTCATGAAACTTACCGATCAATTGTCTGACGTTTTGATGTTCGTCCGGATGTTCCATTTGATAGCTGAACATCAGGc                           <  2:191358/100‑1 (MQ=255)                                                                  gACCGGCACGTTTTGTTGGCGCTCATGAAACTTACCGATCAATTGTCTGACGTTTTGATGTTCGTCCGGATGTTCCATTTGATAGCTGAACATCAGGCAg                         <  2:1128802/100‑1 (MQ=255)                                                                      ggCACGTTTTGTTGGCGCTCATGAAACTTACCGATCAATTGTCTGACGTTTTGATGTTCGTCCGGATGTTCCATTTGATAGCTGAACATCAGGCAGTCaa                     >  1:259085/1‑100 (MQ=255)                                                                      ggCACGTTTTGTTGGCGCTCATGAAACTTACCGATCAATTGTCTGACGTTTTGATGTTCGTCCGGATGTTCCATTTGATAGCTGAACATCAGGCAGTCaa                     >  1:1544781/1‑100 (MQ=255)                                                                      ggCACGTTATGTTGGCGCGCACGAAACCTACCGATCAAGAGTCTGACGTTTTGATGTTCGTCCGGATGTTCCATTTGATAGCTGAACATCAGGAAg                         >  2:763363/1‑96 (MQ=255)                                                                        cACGTTTTGTTGGCGCTTATGAAACTTACCGCTCTATTGGCTGACGTTTTGATTTTCGTCCGGATGTTCCATTTGATAGCTGAACAGCAGGCAGTCAATg                   <  1:1015926/100‑1 (MQ=255)                                                                              ttgttgGCGCTCATGAAACTTACCGATCAATTGTCTGACGTTTTGATGTTCGTCCGGATGTTCCATTTGATAGCTGAACATCAGGCAGTCAATGGCTTCg             <  1:1233010/100‑1 (MQ=255)                                                                               tgttgGCGCTCATGAAACTTACCGATCAATTGTCTGACGTTTTGATGTTCGTCCGGATGTTCCATTTGATAGCTGAACATCAGGCAGTCAATGGCTTCGt            <  1:285603/100‑1 (MQ=255)                                                                                 atctcgcTCATGAAACTTACCGATCAATTGTCTGACGTTTTGATGTTCGTCCGGATGTTCCATTTGATAGCTGAACATCAGGCAGTCAATGGCTTCGttt          <  2:1363163/96‑1 (MQ=255)                                                                                  tgGCGCTCATGAAACTTACCGATCAATTGTCTGACGTTTTGATGTTCGTCCGGATGTTCCATTTGATAGCTGAACATCAGGCAGTCAATGGCTTCGTTTg         <  2:686042/100‑1 (MQ=255)                                                                                    gcgcTCATGAAACTTACCGATCAATTGTCTGACGTTTTGATGTTCGTCCGGATGTTCCATTTGATAGCTGAACATCAGGCAGTCAATGGCTTCGTTTGaa       <  1:510022/100‑1 (MQ=255)                                                                                     cgcTCATGAAACTTACCGATCAATTGTCTGACGTTTTGATGTTCGTCCGGATGTTCCATTTGATAGCTGAACATCAGGCAGTCAATGGCTTCGtttagat      >  1:1363170/1‑96 (MQ=255)                                                                                     cgcTCATGAAACTTACCGATCAATTGTCTGACGTTTTGATGTTCGTCCGGATGTTCCATTTGATAGCTGAACATCAGGCAGTCAATGGCTTCGTTTGAag      <  1:317430/100‑1 (MQ=255)                                                                                       cTCATGAAACTTACCGATCAATTGTCTGATGCTTTGATGTTCGTCCGGATGTTCCATTTGATAGCTCAACATCAGGCAGTCAATGGCTTCGTTTGAagag    <  2:950283/100‑1 (MQ=255)                                                                                        tCATGAAACTTACCGATCAATTGTCTGACGTTTTGATGTTCGTCCGGATGTTCCATTTGATAGCTGAACATCAGGCAGTCAATGGCTTCGTTTGAagaga   <  1:822163/100‑1 (MQ=255)                                                                                         cATGAAACTTACCGATCAATTGTCTGACGTTTTGATGTTCGTCCGGATGTTCCATTTGATAGCTGAACATCAGGCAGTCAATGGCTTCGTTTGAagagag  >  1:1446400/1‑100 (MQ=255)                                                                                               |                                                                                              TCGACAAGCTCCAGCAGGTCGCGATCCATTGCGGCGAGGGCTTTTTCCCGATCGCCCAACAGGAAGACCGGCACGTTTTGTTGGCGCTCATGAAGCTTACCGATCAATTGTCTGACGTTTTGATGTTCGTCCGGATGTTCCATTTGATAGCTGAACATCAGGCAGTCAATGGCTTCGTTTGAAGAGAG  >  NC_000913/4340193‑4340380

Alignment Legend
Aligned base mismatch/match (shaded by quality score): ATCG/ATCG < 3 ≤ ATCG/ATCG < 12 ≤ ATCG/ATCG < 32 ≤ ATCG/ATCG < 41 ≤ ATCG/ATCG
Unaligned base: atcg    Masked matching base: atcg    Alignment gap: ‑    Deleted base: ‑