Predicted mutation
evidence	seq id	position	mutation	freq	annotation	gene	description
RA	AP009048	1,487,675	T→G	9.1%	D948E (GAT→GAG) ‡	hrpA →	ATP‑dependent helicase

Read alignment evidence...
	seq id	position		ref	new	freq	score (cons/poly)	reads	annotation	genes	product
*	AP009048	1,487,675	0	T	G	9.1%	211.5 / 18.6	88	D948E (GAT→GAG) ‡	hrpA	ATP‑dependent helicase
Reads supporting (aligned to +/- strand):  ref base T (39/41);  new base G (3/5);  total (42/46)
Fisher's exact test for biased strand distribution p-value = 7.16e-01
Kolmogorov-Smirnov test that lower quality scores support variant p-value = 7.21e-01

AGCGCGAGTTACGGCGGATGACCGGCGTTACCGTTGACCGCGAAGACTGGCACTGGGATCAGGTGCCCGATCACCTGAAAATTACCTTCCGCGTGGTGGATGACAAAAACAAGAAGCTAAAAGAAGGGCGCTCGCTAC  >  AP009048/1487605‑1487742                                                                       |                                                                    aGCGCGAGTTACGGCGGATGACCGGCGTTACCGTTGACCGCGAAGACTGGCACTGGGATCAGGTGCCCGAt                                                                     <  1:5951117/71‑1 (MQ=255)  gcgcGAGTTACGGCGGATGACCGGCGTTACCGTTGACCGCGAAGACTGGCACTGGGATCAGGTGCCCGATc                                                                    <  1:3452556/71‑1 (MQ=255)  gcgcGAGTTACGGCGGATGACCGGCGTTACCGTTGACCGCGAAGACTGGCACTGGGATCAGGTGCCCGATc                                                                    <  1:7495674/71‑1 (MQ=255)  gcgcGAGTTACGGCGGATGACCGGCGTTACCGTTGACCGCGAAGACTGGCACTGGGATCAGGTGCCCGATc                                                                    <  1:2701393/71‑1 (MQ=255)       aGTTACGGCGGATGACCGGCGTTACCGTTGACCGCGAAGACTGGCACTGGGATCAGGTGCCCGATCACCt                                                                >  1:1670674/1‑70 (MQ=255)       aGTTACGGCGGATGACCGGCGTTACCGTTGACCGCGAAGACTGGCACTGGGATCAGGTGATCGGGCACCTg                                                               <  1:7744435/71‑1 (MQ=255)       aGTTACGGCGGATGACCGGCGTTACCGTTGACCGCGAAGACTGGCACTGGGATCAGGTGATCGGGCACCTg                                                               <  1:5180762/71‑1 (MQ=255)       aGTTACGGCGGATGACCGGCGTTACCGTTGACCGCGAAGACTGGCACTGGGATCAGGTGATCGGGCACCTg                                                               <  1:6007892/71‑1 (MQ=255)       aGTTACGGCGGATGACCGGCGTTACCGTTGACCGCGAAGACTGGCACTGGGATCAGGTGATCGGGCACCTg                                                               <  1:7225572/71‑1 (MQ=255)        gTTACGGCGGATGACCGGCGTTACCGTTGACCGCGAAGACTGGCACTGGGATCAGGTGCCCGATCACCTg                                                               >  1:7078267/1‑70 (MQ=255)        gTTACGGCGGATGACCGGCGTTACCGTTGACCGCGAAGACTGGCACTGGGATCAGGTGCCCGATCACCTg                                                               >  1:64885/1‑70 (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)              gcggATGACCGGCGTTACCGTTGACCGCGAAGACTGGCACTGGGATCAGGTGCCCGATCACCTGAAAATTa                                                        >  1:2967447/1‑71 (MQ=255)                     aCCGGCGTTACCGTTGACCGCGAAGACTGGCACTGGGATCAGGTGCCCGATCACCTGaa                                                             <  1:2728641/59‑1 (MQ=255)                     aCCGGCGTTACCGTTGACCGCGAAGACTGGCACTGGGATCAGGTGCCCGATCACCTGAAAATTACCTTcc                                                  <  1:5195527/70‑1 (MQ=255)                      ccGGCGTTACCGTTGACCGCGAAGACTGGCACTGGGATCAGGTGCCCGATCACCTGAAAATTACCTTCcgc                                                >  1:710818/1‑71 (MQ=255)                      ccGGCGTTACCGTTGACCGCGAAGACTGGCACTGGGATCAGGTGCCCGATCACCTGAAAATTACCTTCcgc                                                >  1:7391134/1‑71 (MQ=255)                       cGGCGTTACCGTTGACCGCGAAGACTGGCACTGGGATCAGGTGCCCGATCACCTGaa                                                             <  1:5961961/57‑1 (MQ=255)                        ggCGTTACCGTTGACCGCGAAGACTGGCACTGGGATCAGGTGCCCGATCa                                                                   <  1:5239393/50‑1 (MQ=255)                        ggCGTTACCGTTGACCGCGAAGACTGGCACTGGGATCAGGTGCCCGATCACCTGAAAATTACCTTCCGCgt                                              >  1:3579691/1‑71 (MQ=255)                        ggCGTTACCGTTGACCGCGAAGACTGGCACTGGGATCAGGTGCCCGATCACCTGAAAATTACCTTCCGCgt                                              <  1:916181/71‑1 (MQ=255)                        ggCGTTACCGTTGACCGCGAAGACTGGCACTGGGATCAGGTGCCCGATCACCTGAAAATTACCTTCCGCgt                                              <  1:495828/71‑1 (MQ=255)                        ggCGTTACCGTTGACCGCGAAGACTGGCACTGGGATCAGGTGCCCGATCACCTGAAAATTACCTTCCGCgt                                              >  1:997899/1‑71 (MQ=255)                         gCGTTACCGTTGACCGCGAAGACTGGCACTGGGATCAGGTGCCCGATCACCTGAAAATTACCTTCCGCgtg                                             >  1:2882346/1‑71 (MQ=255)                          cGTTACCGTTGACCGCGAAGACTGGCACTGGGATCAGGTGCCCGATCACCTGAAAATTACCTTCCGCgtgg                                            <  1:4569225/71‑1 (MQ=255)                            ttACCGTTGACCGCGAAGACTGGCACTGGGATCAGGTGCCCGATCACCTGAAAATTACCTTCCGCgtggtg                                          <  1:260756/71‑1 (MQ=255)                            ttACCGTTGACCGCGAAGACTGGCACTGGGATCAGGTGCCCGATCACCTGAAAATTACCTTCCGCgtggtg                                          <  1:845318/71‑1 (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                                        >  1:6586930/1‑71 (MQ=255)                              aCCGTTGACCGCGAAGACTGGCACTGGGATCAGGTGCCCGATCACCTGAAAATTACCTTCCGCGTGGTGGa                                        >  1:2293798/1‑71 (MQ=255)                              aCCGTTGACCGCGAAGACTGGCACTGGGATCAGGTGCCCGATCACCTGAAAATTACCTTCCGCGTGGTGGa                                        >  1:6148718/1‑71 (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                                                              >  1:5955247/1‑44 (MQ=18)                                   tGACCGCGAAGACTGGCACTGGGATCAGGTGATCGGGCACCTGa                                                              >  1:1254159/1‑44 (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                            <  1:1771515/71‑1 (MQ=255)                                          gAAGACTGGCACTGGGATCAGGTGCCCGATCACCTGAAAATTACCTTCCGCGTGGTGGATGACAAAAACaa                            <  1:5528749/71‑1 (MQ=255)                                          gAAGACTGGCACTGGGATCAGGTGCCCGATCACCTGAAAATTACCTTCCGCGTGGTGGATGACAAAAACaa                            <  1:992240/71‑1 (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                                 >  1:1191918/1‑42 (MQ=255)                                                                  cccGATCACCTGAAAATTACCTTCCGCGTGGTGGATGACaaa                                 >  1:5341575/1‑42 (MQ=255)                                                                   ccGATCACCTGAAAATTACCTTCCGCGTGGTGGATGACAAAAACAAGAAGCTAAAAGAAGGGCGCTCTCTa   >  1:4895832/1‑71 (MQ=255)                                                                     gATCACTTGAAAATTACCTTCCGCGTGGTGGATGACAAAAACaaga                          >  1:7347729/1‑46 (MQ=255)                                                                     gATCACCTGAAAATTACCTTCCGCGTGGTGGATGACAAAAACAAGAAGCTAAAAGAAGGGCGCTCGCTAc  >  1:4958864/1‑70 (MQ=255)                                                                      aTCACCTGAAAATTACCTTCCGCGTGGTGGATGACAAAAACAAGAAGCTAAAAGAAGGGCGCTCGCTAc  >  1:4507483/1‑69 (MQ=255)                                                                      aTCACCTGAAAATTACCTTCCGCGTGGTGGATGACAAAAACAAGAAGCTAAAAGAAGGGCGCTCGCTAc  >  1:3376165/1‑69 (MQ=255)                                                                       tCACCTGAAAATTACCTTCCGCGTGGTGGATGACAAAAACAAGAAGCTAAAAGAAGGGCGCTCGCTAc  >  1:954249/1‑68 (MQ=255)                                                                       |                                                                    AGCGCGAGTTACGGCGGATGACCGGCGTTACCGTTGACCGCGAAGACTGGCACTGGGATCAGGTGCCCGATCACCTGAAAATTACCTTCCGCGTGGTGGATGACAAAAACAAGAAGCTAAAAGAAGGGCGCTCGCTAC  >  AP009048/1487605‑1487742

Alignment Legend
Aligned base mismatch/match (shaded by quality score): ATCG/ATCG < 3 ≤ ATCG/ATCG < 27 ≤ ATCG/ATCG < 32 ≤ ATCG/ATCG < 36 ≤ ATCG/ATCG
Unaligned base: atcg    Masked matching base: atcg    Alignment gap: ‑    Deleted base: ‑