Predicted mutation
evidence	seq id	position	mutation	freq	annotation	gene	description
RA	AP009048	2,124,804	T→C	9.3%	N105D (AAC→GAC)	cpsG ←	phosphomannomutase

Read alignment evidence...
	seq id	position		ref	new	freq	score (cons/poly)	reads	annotation	genes	product
*	AP009048	2,124,804	0	T	C	9.3%	148.3 / 6.9	55	N105D (AAC→GAC)	cpsG	phosphomannomutase
Reads supporting (aligned to +/- strand):  ref base T (37/12);  new base C (2/3);  total (40/15)
Fisher's exact test for biased strand distribution p-value = 1.24e-01
Kolmogorov-Smirnov test that lower quality scores support variant p-value = 9.96e-01

TGGACGTCGCGCAGTCCGGTATCTCCGCTGATCGGGCGAGCCCCCTCGCGAACCAGCTTCATGCCGTTATAATCCATCGGATTATGGCTGGCGGTAACTTCAATGCCGCCATCCACGCCGAGATGGAACGTGGCG  >  AP009048/2124737‑2124871                                                                    |                                                                    tGGACGTCGCGCAGTCCGGTATCTCCGCTGATCGGGCGAGCCCCCTCGCGAACCAGCTTCATGCCGTtat                                                                   >  1:3261104/1‑70 (MQ=255) tGGACGTCGCGCAGTCCGGTATCTCCGCTGATCGGGCGAGCCCCCTCGCGAACCAGCTTCATGCCGTtat                                                                   >  1:419692/1‑70 (MQ=255)    aCGTCGCGCAGTCCGGTATCTCCGCTGATCGGGCGAGCCCCCTCGCGAACCAGCTTCATGCCGTTATAATc                                                               >  1:4140668/1‑71 (MQ=255)    aCGTCGCGCAGTCCGGTATCTCCGCTGATCGGGCGAGCCCCCTCGCGAACCAGCTTCATGCCGTTATAATc                                                               >  1:4146615/1‑71 (MQ=255)      gTCGCGCAGTCCGGTATCTCCGCTGATCGGGCGAGCCCCCTCGCGAACCAGCTTCATGCCGTCATAATccg                                                             <  1:2536070/71‑2 (MQ=255)      gTCGCGCAGTCCGGTATCTCCGCTGATCGGGCGAGCCCCCTCGCGAACCAGCTTCATGCCGTCATAATccg                                                             <  1:14463/71‑2 (MQ=255)         gcgcAGTCCGGTATCTCCGCTGATCGGGCGAGCCCCCTCGCGAACCAGCTTCATGCCGTTATAATCCATCg                                                          >  1:785188/1‑71 (MQ=255)          cgcAGTCCGGTATCTCCGCTGATCGGGCGAGCCCCCTCGCGAACCAGCTTCATGCCGTTATAATCCATCg                                                          >  1:1724556/1‑70 (MQ=255)          cgcAGTCCGGTATCTCCGCTGATCGGGCGAGCCCCCTCGCGAACCAGCTTCATGCCGTTATAATCCATCg                                                          <  1:3453664/70‑1 (MQ=255)            cAGTCCGGTATCTCCGCTGATCGGGCGAGCCCCCTCGCGAACCAGCTTCATGCCGTTATAATCCATCGGAt                                                       >  1:1893587/1‑71 (MQ=255)             aGTCCGGTATCTCCGCTGATCGGGCGAGCCCCCTCGCGAACCAGCTTCATGCCGTTATAATCCATCGGAt                                                       >  1:4255504/1‑70 (MQ=255)              gTCCGGTATCTCCGCTGATCGGGCGAGCCCCCTCGCGAACCAGCTTCATGCCGTtat                                                                   <  1:4330063/57‑1 (MQ=255)               tCCGGTATCTCCGCTGATCGGGCGAGCCCCCTCGCGAACCAGCTTCATGCCGTTATAATCCATCGGATTAt                                                    >  1:4888830/1‑71 (MQ=255)                 cGGTATCTCCGCTGATCGGGCGAGCCCCCTCGCGAACCAGCTTCATGCCGTTATAATCCATCg                                                          >  1:165682/1‑63 (MQ=255)                   gTATCTCCGCTGATCGGGCGAGCCCCCTCGCGAACCAGCTTCATGCCGTTATAATCCATCGGATTAtggct                                                >  1:1270323/1‑71 (MQ=255)                        tcCGCTGATCGGGCGAGCCCCCTCGCGAACCAGCTTCATGCCGTTATAATCCATCGGATTATGGCTGGCgg                                           >  1:4782289/1‑71 (MQ=255)                        tcCGCTGATCGGGCGAGCCCCCTCGCGAACCAGCTTCATGCCGTTATAATCCATCGGATTATGGCTGGCgg                                           >  1:677172/1‑71 (MQ=255)                          cGCTGATCGGGCGAGCCCCCTCGCGAACCAGCTTCATGCCGTTATAAt                                                                >  1:1216257/1‑48 (MQ=255)                          cGCTGATCGGGCGAGCCCCCTCGCGAACCAGCTTCATGCCGTTATAAt                                                                >  1:530795/1‑48 (MQ=255)                          cGCTGATCGGGCGAGCCCCCTCGCGAACCAGCTTCATGCCGTTATAATCCATCGGATTATGGCTGGCgg                                           <  1:4817413/69‑1 (MQ=255)                          cGCTGATCGGGCGAGCCCCCTCGCGAACCAGCTTCATGCCGTTATAATCCATCGGATTATGGCTGGCGGt                                          >  1:1399690/1‑70 (MQ=255)                          cGCTGATCGGGCGAGCCCCCTCGCGAACCAGCTTCATGCCGTTATAATCCATCGGATTATGGCTGGCGGt                                          >  1:1558540/1‑70 (MQ=255)                          cGCTGATCGGGCGAGCCCCCTCGCGAACCAGCTTCATGCCGTTATAATCCATCGGATTATGGCTGGCGGt                                          >  1:2147212/1‑70 (MQ=255)                          cGCTGATCAGGCGAGCCCCCTCGCGAACCAGCTTCATGCCGTTATAATCCATCGGATTATGGCTGGCGGt                                          <  1:3351432/70‑1 (MQ=255)                           gCTGATCGGGCGAGCCCCCTCGCGAACCAGCTTCATGCCGTTATAATCCATCGGATTATGGCTGGCGGTaa                                        <  1:1858093/71‑1 (MQ=255)                              gATCGGGCGAGCCCCCTCGCGAACCAGCTTCATGCCGTTATAATCCATCGGATTa                                                     >  1:5126209/1‑55 (MQ=255)                                  gggCGAGCCCCCTCGCGAACCAGCTTCATGCCGTAATAATCCAGCGGATTATGGCTGGCGGAAACTTCaa                                  >  1:680952/1‑70 (MQ=255)                                    gCGAGCCCCCTCGCGAACCAGCTTCATGCCGTTATAATCCATCGGATTATGGCTGGCGGTAACTTCAATgc                               >  1:3092148/1‑71 (MQ=255)                                        gCCCCCTCGCGAACCAGCTTCATGCCGTTATAATCCATCGGAt                                                       >  1:2595128/1‑43 (MQ=255)                                            ccTCGCGAACCAGCTTCATGCCGTTATAATCCATCGGATTATGGCTGGCgtt                                          <  1:941908/52‑3 (MQ=255)                                            ccTCGCGAACCAGCTTCATGCCGTCATAATCCGATGGATTAt                                                    <  1:1794521/42‑1 (MQ=21)                                              tCGCGAACCAGCTTCATGCCGTTATAATCCATCGGAt                                                       <  1:501958/37‑1 (MQ=255)                                              tCGCGAACCAGCTTCATGCCGTTATAATCCATCGGATTATGGCTGGCGGTAACTTCAATGCCGCCATCCa                      >  1:558856/1‑70 (MQ=255)                                              tCGCGAACCAGCTTCATGCCGTTATAATCCATCGGATTATGGCTGGCGGTAACTTCAATGCCGCCATCCAc                     >  1:1724150/1‑71 (MQ=255)                                              tCGCGAACCAGCTTCATGCCGTTATAATCAATCGGATTATGGATGGCg                                            >  1:2878418/1‑48 (MQ=39)                                              tCGCGAACCAGCTTCATGCCGTCATAATCCGATGGATTAtaa                                                  >  1:1770072/1‑40 (MQ=17)                                              tCGCGAACCAGCTTCATGCCGTCATAATCCGATGGATTAtaa                                                  >  1:4538865/1‑40 (MQ=17)                                               cgcgAACCAGCTTCATGCCGTTATAATCCATCGGATTAtgg                                                  >  1:3014188/1‑41 (MQ=255)                                                gcgAACCAGCTTCATGCCGTTATAATCCATCGGATTATGGCTGGCGGTAACTTCaa                                  >  1:2213583/1‑56 (MQ=255)                                                gcgAACCAGCTTCATGCCGTTATAATCCATCGGATTATGGCTGGCGGTAACTTCaa                                  >  1:3533595/1‑56 (MQ=255)                                                gcgAACCAGCTTCATGCCGTTATAATCCATCGGATTATGGCTGGCGGTAACTTCAATGCCGCCATCCACGc                   >  1:856133/1‑71 (MQ=255)                                                  gAACCAGCTTCATGCCGTTATAATCCATCGGATTa                                                     >  1:3681817/1‑35 (MQ=255)                                                   aaCCAGCTTCATGCCGTTATAATCCATCGGATTATGGCTGGCGGTAACTTCAATGCCGCCATCCACGcc                  >  1:4632099/1‑69 (MQ=255)                                                    aCCAGCTTCATGCCGTTATAATCCATCGGATTATGGCTGGCGGTAACTTCAATGCCGCCATCCACGcc                  >  1:1178739/1‑68 (MQ=255)                                                     ccAGCTTCATGCCGTTATAATCCATCGGATTATGGCTGGCGGTAACTTCAATGCCGCCATCCACGcc                  >  1:744654/1‑67 (MQ=255)                                                     ccAGCTTCATGCCGTTATAATCCATCGGATTATGGCTGGCGGTAACTTCAATGCCGCCATCCACGCCgaga              <  1:5175086/71‑1 (MQ=255)                                                      cAGCTTCATGCCGTTATAATCCATCGGATTATGGCTGGCGGTAACt                                      <  1:3234314/46‑1 (MQ=255)                                                       aGCTTCATGCCGTTATAATCCATCGGATTATGGCTGGCGGTAACTTCAATGCCGCCATCCACGCCGAGATg            >  1:3448658/1‑71 (MQ=255)                                                        gCTTCATGCCGTTATAATCCATCGGATTATGGCTGGCGGTAACTTCaa                                  >  1:977954/1‑48 (MQ=255)                                                        gCTTCATGCCGTTATAATCCATCGGATTATGGCTGGCGGTAACTTCAATg                                >  1:2732207/1‑50 (MQ=255)                                                        gCTTCATGCCGTTATAATCCATCGGATTATGGCTGGCGGTAACTTCAATGCCGCCATCCACGCCGAGATg            >  1:4221058/1‑70 (MQ=255)                                                        gCTTCATGCCGTTATAATCCATCGGATTATGGCTGGCGGTAACTTCAATGCCGCCATCCACGCCGAGATg            >  1:3532679/1‑70 (MQ=255)                                                        gCTTCATGCCGTTATAATCCATCGGATTATGGCTGGCGGTAACTTCAATGCCGCCATCCACGCCGAGATg            >  1:3028309/1‑70 (MQ=255)                                                            cATGCCGTTATAATCCATCGGATTATGGCTGGCGGTAACTTCAATGCCGCCATCCACGCCGAGATGGaa         <  1:661371/69‑1 (MQ=255)                                                             aTGCCGTTATAATCCATCTGATTATGGCTGGCGGTAACTTCAATGCCGCCATCCACGCCGAGATGGAACg       <  1:1810641/70‑1 (MQ=255)                                                             aTGCCGTTATAATCCATCGGATTATGGCTGGCGGTAACTTCAATGCCGCCATCCACGCCGAGATGGAACg       <  1:4373604/70‑1 (MQ=255)                                                              tGCCGTTATAATCCATCGGATTATGGCTGGCGGTAACTTCAATGCCGCCATCCACGCCGAGATGGAACGTg     >  1:2622784/1‑71 (MQ=255)                                                                 cGTTATAATCCATCGGATTATGGCTGGCGGTAACTTCAATGCCGCCATCCACGCCGAGATGGAACGTggaa  <  1:1352701/71‑3 (MQ=255)                                                                   ttATAATCCATCGGATTATGGCTGGCGGTAACTTCAATGCCGCCATCCACGCCGAGATGGAACg       <  1:2586809/64‑1 (MQ=255)                                                                    |                                                                    TGGACGTCGCGCAGTCCGGTATCTCCGCTGATCGGGCGAGCCCCCTCGCGAACCAGCTTCATGCCGTTATAATCCATCGGATTATGGCTGGCGGTAACTTCAATGCCGCCATCCACGCCGAGATGGAACGTGGCG  >  AP009048/2124737‑2124871

Alignment Legend
Aligned base mismatch/match (shaded by quality score): ATCG/ATCG < 3 ≤ ATCG/ATCG < 14 ≤ ATCG/ATCG < 32 ≤ ATCG/ATCG < 36 ≤ ATCG/ATCG
Unaligned base: atcg    Masked matching base: atcg    Alignment gap: ‑    Deleted base: ‑