Predicted mutation
evidence	seq id	position	mutation	freq	annotation	gene	description
RA	AP009048	1,487,671	C→T	9.0%	P947L (CCC→CTC) ‡	hrpA →	ATP‑dependent helicase

Read alignment evidence...
	seq id	position		ref	new	freq	score (cons/poly)	reads	annotation	genes	product
*	AP009048	1,487,671	0	C	T	9.0%	274.7 / 12.3	89	P947L (CCC→CTC) ‡	hrpA	ATP‑dependent helicase
Reads supporting (aligned to +/- strand):  ref base C (32/49);  new base T (3/5);  total (35/54)
Fisher's exact test for biased strand distribution p-value = 1.00e+00
Kolmogorov-Smirnov test that lower quality scores support variant p-value = 9.91e-01

TGAGCGCGAGTTACGGCGGATGACCGGCGTTACCGTTGACCGCGAAGACTGGCACTGGGATCAGGTGCCCGATCACCTGAAAATTACCTTCCGCGTGGTGGATGACAAAAACAAGAAGCTAAAAGAAGGGCGCTCGCTA  >  AP009048/1487603‑1487741                                                                     |                                                                       tGAGCGCGAGTTACGGCGGATGACCGGCGTTACCGTTGACCGCGAAGACTGGCACTGGGATCAGGTGccc                                                                       >  1:3956207/1‑70 (MQ=255)  gAGCGCGAGTTACGGCGGATGACCGGCGTTACCGTTGACCGCGAAGACTGGCACTGGGATCAGGTGccc                                                                       <  1:3055892/69‑1 (MQ=255)  gAGCGCGAGTTACGGCGGATGACCGGCGTTACCGTTGACCGCGAAGACTGGCACTGGGATCAGGTGccc                                                                       <  1:1894826/69‑1 (MQ=255)  gAGCGCGAGTTACGGCGGATGACCGGCGTTACCGTTGACCGCGAAGACTGGCACTGGGATCAGGTGCCCg                                                                      <  1:1233806/70‑1 (MQ=255)  gAGCGCGAGTTACGGCGGATGACCGGCGTTACCGTTGACCGCGAAGACTGGCACTGGGATCAGGTGCCCg                                                                      <  1:5615977/70‑1 (MQ=255)  gAGCGCGAGTTACGGCGGATGACCGGCGTTACCGTTGACCGCGAAGACTGGCACTGGGATCAGGTGCCCg                                                                      <  1:5277501/70‑1 (MQ=255)   aGCGCGAGTTACGGCGGATGACCGGCGTTACCGTTGACCGCGAAGACTGGCACTGGGATCAGGTGCCCGAt                                                                    <  1:5951117/71‑1 (MQ=255)    gcgcGAGTTACGGCGGATGACCGGCGTTACCGTTGACCGCGAAGACTGGCACTGGGATCAGGTGCCCGATc                                                                   <  1:2701393/71‑1 (MQ=255)    gcgcGAGTTACGGCGGATGACCGGCGTTACCGTTGACCGCGAAGACTGGCACTGGGATCAGGTGCCCGATc                                                                   <  1:3452556/71‑1 (MQ=255)    gcgcGAGTTACGGCGGATGACCGGCGTTACCGTTGACCGCGAAGACTGGCACTGGGATCAGGTGCCCGATc                                                                   <  1:7495674/71‑1 (MQ=255)         aGTTACGGCGGATGACCGGCGTTACCGTTGACCGCGAAGACTGGCACTGGGATCAGGTGCCCGATCACCt                                                               >  1:1670674/1‑70 (MQ=255)         aGTTACGGCGGATGACCGGCGTTACCGTTGACCGCGAAGACTGGCACTGGGATCAGGTGATCGGGCACCTg                                                              <  1:5180762/71‑1 (MQ=255)         aGTTACGGCGGATGACCGGCGTTACCGTTGACCGCGAAGACTGGCACTGGGATCAGGTGATCGGGCACCTg                                                              <  1:7744435/71‑1 (MQ=255)         aGTTACGGCGGATGACCGGCGTTACCGTTGACCGCGAAGACTGGCACTGGGATCAGGTGATCGGGCACCTg                                                              <  1:6007892/71‑1 (MQ=255)         aGTTACGGCGGATGACCGGCGTTACCGTTGACCGCGAAGACTGGCACTGGGATCAGGTGATCGGGCACCTg                                                              <  1:7225572/71‑1 (MQ=255)          gTTACGGCGGATGACCGGCGTTACCGTTGACCGCGAAGACTGGCACTGGGATCAGGTGCCCGATCACCTg                                                              >  1:64885/1‑70 (MQ=255)          gTTACGGCGGATGACCGGCGTTACCGTTGACCGCGAAGACTGGCACTGGGATCAGGTGCCCGATCACCTg                                                              >  1:7078267/1‑70 (MQ=255)          gTTACGGCGGATGACCGGCGTTACCGTTGACCGCGAAGACTGGCACTGGGATCAGGTGCCCGATCACCTGa                                                             <  1:2019851/71‑1 (MQ=255)          gTTACGGCGGATGACCGGCGTTACCGTTGACCGCGAAGACTGGCACTGGGATCAGGTGATCGGGCACCTg                                                              <  1:2047778/70‑1 (MQ=255)           ttACGGCGGATGACCGGCGTTACCGTTGACCGCGAAGACTGGCACTGGGATCAGGTGCCCGATCACCTGaa                                                            <  1:1611861/71‑1 (MQ=255)           ttACGGCGGATGACCGGCGTTACCGTTGACCGCGAAGACTGGCACTGGGATCAGGTGCCCGATCACCTGa                                                             >  1:5315258/1‑70 (MQ=255)             aCGGCGGATGACCGGCGTTACCGTTGACCGCGAAGACTGGCACTGGGATCAGGTGCCCGATCACCTGaaaa                                                          >  1:1573174/1‑71 (MQ=255)             aCGGCGGATGACCGGCGTTACCGTTGACCGCGAAGACTGGCACTGGGATCAGGTGCCCGATCACCTGaaa                                                           >  1:6247689/1‑70 (MQ=255)              cggcggATGACCGGCGTTACCGTTGACCGCGAAGACTGGCACTGGGATCAGGTGCCCGATCACCTGAAAAt                                                         <  1:6521244/71‑1 (MQ=255)              cggcggATGACCGGCGTTACCGTTGACCGCGAAGACTGGCACTGGGATCAGGTGCCCGATCACCTGAAAAt                                                         <  1:2316046/71‑1 (MQ=255)               ggcggATGACCGGCGTTACCGTTGACCGCGAAGACTGGCACTGGGATCAGGTGCCCGATCACCTGAAAAtt                                                        <  1:2617282/71‑1 (MQ=255)                gcggATGACCGGCGTTACCGTTGACCGCGAAGACTGGCACTGGGATCAGGTGCCCGa                                                                     <  1:3344649/57‑1 (MQ=255)                gcggATGACCGGCGTTACCGTTGACCGCGAAGACTGGCACTGGGATCAGGTGCCCGATCACCTGAAAATTa                                                       >  1:2967447/1‑71 (MQ=255)                     tGACCGGCGTTACCGTTGACCGCGAAGACTGGCACTGGGATCAGGTGCCCg                                                                      <  1:343932/51‑1 (MQ=255)                       aCCGGCGTTACCGTTGACCGCGAAGACTGGCACTGGGATCAGGTGCCCGATCACCTGaa                                                            <  1:2728641/59‑1 (MQ=255)                       aCCGGCGTTACCGTTGACCGCGAAGACTGGCACTGGGATCAGGTGCCCGATCACCTGAAAATTACCTTcc                                                 <  1:5195527/70‑1 (MQ=255)                        ccGGCGTTACCGTTGACCGCGAAGACTGGCACTGGGATCAGGTGCCCGATCACCTGAAAATTACCTTCcgc                                               >  1:7391134/1‑71 (MQ=255)                        ccGGCGTTACCGTTGACCGCGAAGACTGGCACTGGGATCAGGTGCCCGATCACCTGAAAATTACCTTCcgc                                               >  1:710818/1‑71 (MQ=255)                         cGGCGTTACCGTTGACCGCGAAGACTGGCACTGGGATCAGGTGCCCGATCACCTGaa                                                            <  1:5961961/57‑1 (MQ=255)                          ggCGTTACCGTTGACCGCGAAGACTGGCACTGGGATCAGGTGCCCGATCa                                                                  <  1:5239393/50‑1 (MQ=255)                          ggCGTTACCGTTGACCGCGAAGACTGGCACTGGGATCAGGTGCCCGATCACCTGAAAATTACCTTCCGCgt                                             >  1:997899/1‑71 (MQ=255)                          ggCGTTACCGTTGACCGCGAAGACTGGCACTGGGATCAGGTGCCCGATCACCTGAAAATTACCTTCCGCgt                                             <  1:916181/71‑1 (MQ=255)                          ggCGTTACCGTTGACCGCGAAGACTGGCACTGGGATCAGGTGCCCGATCACCTGAAAATTACCTTCCGCgt                                             <  1:495828/71‑1 (MQ=255)                          ggCGTTACCGTTGACCGCGAAGACTGGCACTGGGATCAGGTGCCCGATCACCTGAAAATTACCTTCCGCgt                                             >  1:3579691/1‑71 (MQ=255)                           gCGTTACCGTTGACCGCGAAGACTGGCACTGGGATCAGGTGCCCGATCACCTGAAAATTACCTTCCGCgtg                                            >  1:2882346/1‑71 (MQ=255)                            cGTTACCGTTGACCGCGAAGACTGGCACTGGGATCAGGTGCCCGATCACCTGAAAATTACCTTCCGCgtgg                                           <  1:4569225/71‑1 (MQ=255)                              ttACCGTTGACCGCGAAGACTGGCACTGGGATCAGGTGCCCGa                                                                     <  1:5913803/43‑1 (MQ=255)                              ttACCGTTGACCGCGAAGACTGGCACTGGGATCAGGTGCCCGa                                                                     <  1:4234627/43‑1 (MQ=255)                              ttACCGTTGACCGCGAAGACTGGCACTGGGATCAGGTGCCCGATCACCTGAAAATTACCTTCCGCgtggtg                                         <  1:845318/71‑1 (MQ=255)                              ttACCGTTGACCGCGAAGACTGGCACTGGGATCAGGTGCCCGATCACCTGAAAATTACCTTCCGCgtggtg                                         <  1:260756/71‑1 (MQ=255)                               tACCGTTGACCGCGAAGACTGGCACTGGGATCAGGTGccc                                                                       <  1:4045767/40‑1 (MQ=255)                               tACCGTTGACCGCGAAGACTGGCACTGGGATCAGGTGCCCGATCACCTGAAAATTACCTTCCGCgtggtg                                         >  1:1139745/1‑70 (MQ=255)                                aCCGTTGACCGCGAAGACTGGCACTGGGATCAGGTGCCCGATCACCTGAAAATTACCTTcc                                                 >  1:5533571/1‑61 (MQ=255)                                aCCGTTGACCGCGAAGACTGGCACTGGGATCAGGTGCCCGATCACCTGAAAATTACCTTCCGCgtggt                                          >  1:3347588/1‑68 (MQ=255)                                aCCGTTGACCGCGAAGACTGGCACTGGGATCAGGTGCCCGATCACCTGAAAATTACCTTCCGCGtggtgg                                        <  1:7879994/70‑1 (MQ=255)                                aCCGTTGACCGCGAAGACTGGCACTGGGATCAGGTGCCCGATCACCTGAAAATTACCTTCCGCGTGGTGGa                                       >  1:6148718/1‑71 (MQ=255)                                aCCGTTGACCGCGAAGACTGGCACTGGGATCAGGTGCCCGATCACCTGAAAATTACCTTCCGCGTGGTGGa                                       >  1:6586930/1‑71 (MQ=255)                                aCCGTTGACCGCGAAGACTGGCACTGGGATCAGGTGCCCGATCACCTGAAAATTACCTTCCGCGTGGTGGa                                       >  1:2293798/1‑71 (MQ=255)                                 ccGTTGACCGCGAAGACTTGCACTGGGATCAGGTGCCCGATCACCTGAAAATTACCTTCCGCGTGGTGGa                                       <  1:5387367/70‑1 (MQ=255)                                 ccGTTGACCGCGAAGACTGGCACTGGGATCAGGTGCCCGATCACCTGAAAATTACCTTCCGCGTGGTGGa                                       <  1:3267393/70‑1 (MQ=255)                                   gTTGACCGCGAAGACTGGCACTGGGATCAGGTGCCCGATCACCTGAAAATTAcc                                                     >  1:6488122/1‑54 (MQ=255)                                   gTTGACCGCGAAGACTGGCACTGGGATCAGGTGCCCGATCACCTGAAAATTACCTTCCGCGTGGTGGATGa                                    <  1:2102584/71‑1 (MQ=255)                                   gTTAACCGCGAAGACTGGCACTGGGATCAGGTGCCCGATCGCCTGAAAATTACCTTCCGCGTGGTGGATGa                                    >  1:3678505/1‑71 (MQ=255)                                   gTTAACCGCGAAGACTGGCACTGGGATCAGGTGCCCGATCACCTGAAAATTACCTTCCGCGTGGTGGATGa                                    >  1:4750345/1‑71 (MQ=255)                                     tGACCGCGAAGACTGGCACTGGGATCAGGTGATCGGGCACCTGa                                                             >  1:1606156/1‑44 (MQ=18)                                     tGACCGCGAAGACTGGCACTGGGATCAGGTGATCGGGCACCTGa                                                             >  1:1254159/1‑44 (MQ=18)                                     tGACCGCGAAGACTGGCACTGGGATCAGGTGATCGGGCACCTGa                                                             >  1:5955247/1‑44 (MQ=18)                                      gACCGCGAAGACTGGCACTGGGATCAGGTGCCCGATCACCTGAAAATTACCTTCCGCGTGGTGGATGACa                                  <  1:6633756/70‑1 (MQ=255)                                      gACCGCGAAGACTGGCACTGGGATCAGGTGCCCGATCACCTGAAAATTACCTTCCGCGTGGTGGATGACa                                  <  1:2707354/70‑1 (MQ=255)                                       tccGCGAAGACTGGCACTGGGATCAGGTGCCCGATCACCTGAAAATTACCTTCCGCGtggtgg                                        <  1:3552420/62‑1 (MQ=255)                                       aCCGCGAAGACTGGCACTTGGATCAGGTGCCCGATCACCTGAAAATTACCTTCCGCGTGGTGGATGACaa                                 <  1:2994608/70‑1 (MQ=255)                                       aCCGCGAAGACTGGCACTGGGATCAGGTGCCCGATCAcc                                                                <  1:2070807/39‑1 (MQ=255)                                         cgcgAAGACTGGCACTGGGATCAGGTGCCCGATCACCTGAAAATTACCTTCCGCGTGGTGGATGACaaaaa                              >  1:98323/1‑71 (MQ=255)                                           cgAAGACTGGCACTGGGATCAGGTGCCCGATCACCTGAAAATTACCTTCCGCGTGGTGGATGACAAAAAc                             >  1:2819915/1‑70 (MQ=255)                                            gAAGACTGGCACTGGGATCAGGTGCCCGATCACCTGaa                                                            <  1:4432188/38‑1 (MQ=255)                                            gAAGACTGGCACTGGGATCAGGTGCCCGATCACCTGAAAATTACCTTCCGCGTGGTGGATGACAAAAACaa                           <  1:5528749/71‑1 (MQ=255)                                            gAAGACTGGCACTGGGATCAGGTGCCCGATCACCTGAAAATTACCTTCCGCGTGGTGGATGACAAAAACaa                           <  1:992240/71‑1 (MQ=255)                                            gAAGACTGGCACTGGGATCAGGTGCCCGATCACCTGAAAATTACCTTCCGCGTGGTGGATGACAAAAACaa                           <  1:1771515/71‑1 (MQ=255)                                              aGACTGGCACTGGGATCAGGTGCCCGATCACCTGAAAATTACCTTCCGCGTGGTGGATGACAAAAACaag                          >  1:1859873/1‑70 (MQ=255)                                              aGACTGGCACTGGGATCAGGTGCCCGATCACCTGAAAATTACCTTCCGCGTGGTGGATGACAAAAACaag                          >  1:3439018/1‑70 (MQ=255)                                                aCTGGCACTGGGATCAGGTGCCCGATCACCTGAAAATTACCTTCCGCGTGGTGGATGACAAAAACaa                           <  1:2351710/67‑1 (MQ=255)                                                  tGGCACTGGGATCAGGTGCCCGATCACCTGAAAATTACCTTCCGCGTGGTGGAt                                      >  1:3657512/1‑54 (MQ=255)                                                    gCACTGGGATCAGGTGCCCGATCACCTGAAAATTACCTTCCGCGTGGTGGATGACAAAAACAAGAAGCt                     <  1:5242006/69‑1 (MQ=255)                                                    gCACTGGGATCAGGTGCCCGATCACCTGAAAATTACCTTCCGCGTGGTGGATGACAAAAACAAGAAGCTa                    >  1:341637/1‑70 (MQ=255)                                                       cTGGGATCAGGTGCCCGATCACCTGAAAATTACCTTCcgcg                                              <  1:2315834/41‑1 (MQ=255)                                                       cTGGGATCAGGTGCCCGATCACCTGAAAATTACCTTCCGCGTGGTGGATGACaa                                 <  1:2488400/54‑1 (MQ=255)                                                       cTGGGATCAGGTGCCCGATCACCTGAAAATTACCTTCCGCGTGGTGGATGACAAAAACAAGAAGCTAAaag                <  1:4983453/71‑1 (MQ=255)                                                        tGGGATCAGGTGCCCGATCACCTGAAAATTACCTTCCGCGTGGTGGATGACAAAAACAAGAAGCTAAaag                >  1:1368027/1‑70 (MQ=255)                                                        tGGGATCAGGTGCCCGATCACCTGAAAATTACCTTCCGCGTGGTGGATCACAAAAACAAGAAGCTaaaa                 <  1:5980065/69‑1 (MQ=255)                                                          ggATCAGGTGCCCGATCACCTGAAAATTACCTTCCGCgtg                                            <  1:5648746/40‑1 (MQ=255)                                                           gATCAGGTGCCCGATCACCTGAAAATTACCTTCCGCGTGGTGGATGACAAAAACAAGAAGCTAAAAGAAgg            <  1:5323280/71‑1 (MQ=255)                                                            aTCAGGTGCCCGATCACCTGAAAATTACCTTCCGCGtggtgg                                        >  1:5896503/1‑42 (MQ=255)                                                             tCAGGTGCCCGATCACCTGAAAATTACCTTCCGCGTGGTGGATGACAAAAACaaga                         <  1:1942810/56‑1 (MQ=255)                                                             tCAGGTGCCCGATCACCTGAAAATTACCTTCCGCGTGGTGGATGACAAAAACaag                          >  1:1599657/1‑55 (MQ=255)                                                                ggTGCCCGATCACCTGAAAATTACCTTCCGCGTGGTGGATGACAAAAACAAGAAGCTAAAAGAAGGGcgct       >  1:6499042/1‑71 (MQ=255)                                                                  tGCCCGATCACCTGAAAATTACCTTCCGCGTGGTGGATGACa                                  <  1:7030769/42‑1 (MQ=255)                                                                  tGCCCGATCACCTGAAAATTACCTTCCGCGTGGTGGATGACa                                  <  1:6022403/42‑1 (MQ=255)                                                                   gCCCGATCACCTGAAAATTACCTTCCGCGTGGTGGATGACAAAAACAAGAAGCTAAAAGAAGGGcgctcgc    >  1:2085869/1‑71 (MQ=255)                                                                    cccGATCACCTGAAAATTACCTTCCGCGTGGTGGATGACaaa                                >  1:5341575/1‑42 (MQ=255)                                                                    cccGATCACCTGAAAATTACCTTCCGCGTGGTGGATGACaaa                                >  1:1191918/1‑42 (MQ=255)                                                                     ccGATCACCTGAAAATTACCTTCCGCGTGGTGGATGACAAAAACAAGAAGCTAAAAGAAGGGCGCTCTCTa  >  1:4895832/1‑71 (MQ=255)                                                                     |                                                                       TGAGCGCGAGTTACGGCGGATGACCGGCGTTACCGTTGACCGCGAAGACTGGCACTGGGATCAGGTGCCCGATCACCTGAAAATTACCTTCCGCGTGGTGGATGACAAAAACAAGAAGCTAAAAGAAGGGCGCTCGCTA  >  AP009048/1487603‑1487741

Alignment Legend
Aligned base mismatch/match (shaded by quality score): ATCG/ATCG < 3 ≤ ATCG/ATCG < 21 ≤ ATCG/ATCG < 32 ≤ ATCG/ATCG < 36 ≤ ATCG/ATCG
Unaligned base: atcg    Masked matching base: atcg    Alignment gap: ‑    Deleted base: ‑