Read alignment evidence...
	seq id	position		ref	new	freq	score (cons/poly)	reads	annotation	genes	product
*	NZ_CP009273	1,946,825	0	T	C	65.6%	46.6 / 65.3	62	R101R (CGT→CGC)	yecN	MAPEG family protein
Reads supporting (aligned to +/- strand):  ref base T (7/14);  new base C (23/17);  total (31/31)
Fisher's exact test for biased strand distribution p-value = 1.06e-01
Kolmogorov-Smirnov test that lower quality scores support variant p-value = 6.50e-01
Rejected as consensus: Frequency below/above cutoff threshold.

TGTGCTGATGCTGTTTATGGAAATGAATGGCGCAGAAACCTGGATGGTGCATATTTGCGGCATCGTTTTGCTTGCTGGTCGTCTGATGCATTATTACGGTTTTCATCACCGTCTGTTCCGCTGGCGACGTTCCGGCATGAGCGCCACCTGGTGTGCGCTGTTGCTGATGGTGCTGGCGAATCTTTGGTATATGCCCTGGGAGTTGGTTTTCTCCCTGCGTTAGCGCACAATACGCCACTTTCTTTTTCCCGGATTTTTACGTTA  >  NZ_CP009273/1946696‑1946959                                                                                                                                  |                                                                                                                                       tgtgCTGATGCTGTTTATGGAAATGAATGGCGCAGAAACCTGGATGGTGCATATTTGCGGCATCGTTTTGCTTGCTGGTCGTCTGATGCATTATTACGGTTTTCATCACCGTCTGTTCCGCTGGCGACGCTCCGGCAt                                                                                                                                >  2:588638/1‑138 (MQ=255)   tgCTGATGCTGTTTATGGAAATGAATGGCGCAGAAACCTGGATGGTGCATATTTGCGGCATCGTTTTGCTTGCTGGTCGTCTGATGCATTATTACGGTTTTCATCACCGTCTGTTCCGCTGGCGACGTTCCGGCATGAg                                                                                                                             >  1:917072/1‑139 (MQ=255)     cTGATGCTGTTTATGGAAATGAATGGCGCAGAAACCTGGATGGTGCATATTTGCGGCATCGTTTTGCTTGCTGGTCGTCTGATGCATTATTACGGTTTTCATCACCGTCTGTTCCGCTGGCGACGTTCCGGCATGAgc                                                                                                                            <  1:199730/138‑1 (MQ=255)     cTGATGCTGTTTATGGAAATGAATGGCGCAGAAACCTGGATGGTGCATATTTGCGGCATCGTTTTGCTTGCTGGTCGTCTGATGCATTATTACGGTTTTCATCACCGTCTGTTCCGCTGGCGACGCTCCGGCATGAgc                                                                                                                            <  1:229556/138‑1 (MQ=255)         tGCTGTTTATGGAAATGAATGGCGCAGAAACCTGGATGGTGCATATTTGCGGCATCGTTTTGCTTGCTGGTCGTCTGATGCATTATTACGGTTTTCATCACCGTCTGTTCCGCTGGCGACGTTCCGGCATGAGCGCCAc                                                                                                                       <  2:942134/139‑1 (MQ=255)             gTTTATGGAAATGAATGGCGCAGAAACCTGGATGGTGCATATTTGCGGCATCGTTTTGCTTGCTGGTCGTCTGATGCATTATTACGGTTTTCATCACCGTCTGTTCCGCTGGCGACGCTCCGGCATGAGCGCCACCTgg                                                                                                                   >  1:194904/1‑139 (MQ=255)             gTTTATGGAAATGAATGGCGCAGAAACCTGGATGGTGCATATTTGCGGCATCGTTTTGCTTGCTGGTCGTCTGATGCATTATTACGGTTTTCATCACCGTCTGTTCCGCTGGCGACGCTCCGGCATGAGCGCCACCTgg                                                                                                                   >  1:57389/1‑139 (MQ=255)                  tGGAAATGAATGGCGCAGAAACCTGGATGGTGCATATTTGCGGCATCGTTTTGCTTGCTGGTCGTCTGATGCATTATTACGGTTTTCATCACCGTCTGTTCCGCTGGCGACGCTCCGGCATGAGCGCCACCTGGTGTgc                                                                                                              >  1:84123/1‑139 (MQ=255)                    gAAATGAATGGCGCAGAAACCTGGATGGTGCATATTTGCGGCATCGTTTTGCTTGCTGGTCGTCTGATGCATTATTACGGTTTTCATCACCGTCTGTTCCGCTGGCGACGTTCCGGCATGAGCGCCACCTGGTGTgcg                                                                                                             <  1:813745/138‑1 (MQ=255)                    gAAATGAATGGCGCAGAAACCTGGATGGTGCATATTTGCGGCATCGTTTTGCTTGCTGGTCGTCTGATGCATTATTACGGTTTTCATCACCGTCTGTTCCGCTGGCGACGCTCCGGCATGAGCGTCACCTGGTGTgcg                                                                                                             <  1:1281453/138‑1 (MQ=255)                        tgaatgGCGCAGAAACCTGGATGGTGCATATTTGCGGCATCGTTTTGCTTGCTGGTCGTCTGATGCATTATTACGGTTTTCATCACCGTCTGTTCCGCTGGCGACGCTCCGGCATGAGCGCCACCTGGTGTGCGCTGtt                                                                                                        >  2:1163407/1‑139 (MQ=255)                        tgaatgGCGCAGAAACCTGGATGGTGCATATTTGCGGCATCGTTTTGCTTGCTGGTCGTCTGATGCATTATTACGGTTTTCATCACCGTCTGTTCCGCAGGCGACGCTCCGGCATGAGCGCCCCCTGGTGTGCGCTGtt                                                                                                        >  2:297090/1‑139 (MQ=255)                              gcgcAGAAACCTGGATGGTGCATATTTGCGGCATCGTTTTGCTTGCTGGTCGTCTGATGCATTATTACGGTTTTCATCACCGTCTGTTCCGCTGGCGACGCTCCGGCATGAGCGCCACCTGGTGTGCGCTGTTGCTGa                                                                                                   <  1:583852/138‑1 (MQ=255)                                   gAAACCTGGCTGGTGCATATTTGCGGCATCGTTTTGCTTGCTGGTCGTCTGATGCATTATTACGGTTTTCATCACCGTCTGTTCCGCTGGCGACGTTCCGGCATGAGCGCCACCTGGTGTGCGCTGTTGCTGATGGTGc                                                                                             >  2:630954/1‑139 (MQ=255)                                           gATGGTGCATATTTGCGGCATCGTTTTGCTTGCTGGTCGTCTGATGCATTATTACGGTTTTCATCACCGTCTGTTCCGCTGGCGACGTTCCGGCATGAGCGCCACCTGGTGTGCGCTGTTGCTGATGGTGCTGGCGaa                                                                                      <  2:374062/138‑1 (MQ=255)                                           gATGGTGCATATTTGCGGCATCGTTTTGCTTGCTGGTCGTCTGATGCATTATTACGGTTTTCATCACCGTCTGTTCCGCTGGCGACGTTCCGGCATGAGCGACACCTGGTGTGCGCTGTTGCTGATGGTGCTGGCGAAt                                                                                     <  2:1082094/139‑1 (MQ=255)                                               gTGCATATTTGCGGCATCGTTTTGCTTGCTGGTCGTCTGATGCATTATTACGGTTTTCATCACCGTCTGTTCCGCTGGCGACGTTCCGGCATGAGCGCCACCTGGTGTGCGCTGTTGCTGATGGTGCTGGCGAATCtt                                                                                  <  2:917072/138‑1 (MQ=255)                                               gTGCATATTTGCGGCATCGTTTTGCTTGCTGGTCGTCTGATGCATTATTACGGTTTTCATCACCGTCTGTTCCGCTGGCGACGCTCCGGCATGAGCGCCACCTGGTGTGCGCTGTTGCTGATGGTGCTGGCGAATCttt                                                                                 <  1:751210/139‑1 (MQ=255)                                               gTGCATATTTGCGGCATCGTTTTGCTTGCTGGTCGTCTGATGCATTATTACGGTTTTCATCACCGTCTGTTCCGCTGGCGACGCTCCGGCATGAGCGCCACCTGGTGTGCGCTGTTGCTGATGGTGCTGGCGAATCtt                                                                                  <  2:1205609/138‑1 (MQ=255)                                                tGCATATTTGCGGCATCGTTTTGCTTGCTGGTCGTCTGATGCATTATTACGGTTTTCATCACCGTCTGTTCCGCTGGCGACGTTCCGGCATGAGCGCCACCTGGTGTGCGCTGTTGCTGATGGTGCTGGCGAATCTTTg                                                                                >  1:763201/1‑139 (MQ=255)                                                tGCATATTTGCGGCATCGTTTTGCTTGCTGGTCGTCTGATGCATTATTACGGTTTTCATCACCGTCTGTTCCGCTGGCGACGTTCCGGCATGAGCGCCACCTGGTGTGCGCTGTTGCTGATGGTGCTGGCGAATCTTTg                                                                                >  2:375332/1‑139 (MQ=255)                                                tGCATATTTGCGGCATCGTTTTGCTTGCTGGTCGTCTGATGCATTATTACGGTTTTCATCACCGTCTGTTCCGCTGGCGACGCTCCGGCATGAGCGCCAc                                                                                                                       <  2:1240085/100‑1 (MQ=255)                                                tGCATATTTGCGGCATCGTTTTGCTTGCTGGTCGTCTGATGCATTATTACGGTTTTCATCACCGTCTGTTCCGCTGGCGACGCTCCGGCATGAGCGCCAc                                                                                                                       >  1:1240085/1‑100 (MQ=255)                                                tGCATATTTGCGGCATCGTTTTGCTTGCTGGTCGTCTGATGCATTATTACGGTTTTCATCACCGTCTGTTCCGCTGGCGACGCTCCGGCATGAGCGCCACCTGGTGTGCGCTGTTGCTGa                                                                                                   <  1:1276169/120‑1 (MQ=255)                                                tGCATATTTGCGGCATCGTTTTGCTTGCTGGTCGTCTGATGCATTATTACGGTTTTCATCACCGTCTGTTCCGCTGGCGACGCTCCGGCATGAGCGCCACCTGGTGTGCGCTGTTGCTGa                                                                                                   >  2:1276169/1‑120 (MQ=255)                                                tGCATATTTGCGGCATCGTTTTGCTTGCTGGTCGTCTGATGCATTATTACGGTTTTCATCACCGTCTGTTCCGCTGGCGACGCTCCGGCATGAGCGCCACCTGGTGTGCGCTGTTGCTGa                                                                                                   >  2:237343/1‑120 (MQ=255)                                                tGCATATTTGCGGCATCGTTTTGCTTGCTGGTCGTCTGATGCATTATTACGGTTTTCATCACCGTCTGTTCCGCTGGCGACGCTCCGGCATGAGCGCCACCTGGTGTGCGCTGTTGCTGa                                                                                                   <  1:237343/120‑1 (MQ=255)                                                tGCATATTTGCGGCATCGTTTTGCTTGCTGGTCGTCTGATGCATTATTACGGTTTTCATCACCGTCTGTTCCGCTGGCGACGCTCCGGCATGAGCGCCACCTGGTGTGCGCTGTTGCTGATGGTGCTGGCGAATCTTTg                                                                                >  1:607249/1‑139 (MQ=255)                                                tGCATATTTGCGGCATCGATTTGCTTGCTGGGCGTCTGATGCATTATTACGGTTTTAATCACCGTCTGTTACGCTGGCGACGATCCGGCATGAGCGCCACCTGGTGTGCGCTGTTGCTGATGGGGCTGGCGAATCTTTg                                                                                >  2:14041/1‑139 (MQ=255)                                                  cATATTTGCGGCATCGTTTTGCTTGCTGGTCGTCTGATGCATTATTACGGTTTTCATCACCGTCTGTTCCGCTGGCGACGTTCCGGCATGAGCGCCACCTGGTGTGCGCTGTTGCTGa                                                                                                   <  2:323986/118‑1 (MQ=255)                                                  cATATTTGCGGCATCGTTTTGCTTGCTGGTCGTCTGATGCATTATTACGGTTTTCATCACCGTCTGTTCCGCTGGCGACGTTCCGGCATGAGCGCCACCTGGTGTGCGCTGTTGCTGa                                                                                                   >  1:323986/1‑118 (MQ=255)                                                  cATATTTGCGGCATCGTTTTGCTTGCTGGTCGTCTGATGCATTATTACGGTTTTCATCACCGTCTGTTCCGCTGGCGACGTTCCGGCATGAGCGCCACCTGGTGTGCGCTGTTGCTGATGGTGCTGGCGAATCTTTgg                                                                               >  2:918305/1‑138 (MQ=255)                                                          cGGCATCGTTTTGCTTGCTGGTCGTCTGATGCATTATTACGGTTTTCATCACCGTCTGTTCCGCTGGCGACGCTACGGCATGAGCGCCACCTGGTGTGCGCTGTTGCTGATGGTGCTGGCGAATCTTTGGTATATGccc                                                                      >  1:607221/1‑139 (MQ=255)                                                                 gTTTTGCTTGCTGGTCGTCTGATGCATTATTACGGTTTTCATCACCGTCTGTTCCGCTGGCGACGTTCCGGCATGAGCGCCACCTGGTGTGCGCTGTTGCTGATGGTGCTGGCGAATCTTTGGTATATGCCCTGGGAg                                                                <  1:630954/138‑1 (MQ=255)                                                                 gTTTTGCTTGCTGGTCGTCTGATGCATTATTACGGTTTTCATCACCGTCTGTTCCGCTGGCGACGTTCCGGCATGAGCGCCACCTGGTGTGCGCTGTTGCTGATGGTGCTGGCGAATCTTTGGTATATGCCCTGGGAGt                                                               <  1:918305/139‑1 (MQ=255)                                                                 gTTTTGCTTGCTGGTCGTCTGATGCATTATTACGGTTTTCATCACCGTCTGTTCCGCTGGCGACGCTCCGGCATGAGCGCCACCTGGTGTGCGCTGTTGCTGATGGTGCTGGCGAATCTTTGGTATATGCCCTGGGAg                                                                <  1:588638/138‑1 (MQ=255)                                                                 gTTTTGCTTGCTGGTCGTCTGATGCATTATTACGGTTTTCATCACCGTCTGTTCCGCTGGCGACGCTCCGGCATGAGCGCCACCTGGTGTGCGCTGTTGCTGATGGTGCTGGCGAATCTTTGGTATATGCCCTGGGAg                                                                <  1:726448/138‑1 (MQ=255)                                                                  ttttGCTTGCTGGTCGTCTGATGCATTATTACGGTTTTCATCACCGTCTGTTCCGCTGGCGACGTTCCGGCATGAGCGCCACCTGGTGTGCGCTGTTGCTGATGGTGCTGGCGAATCTTTGGTATATGCCCTGGGAGtt                                                              <  2:901389/139‑1 (MQ=255)                                                                           ctGGTCGTCTGATGCATTATTACGGTTTTCATCACCGTCTGTTCCGCTGGCGACGCTCCGGCATGAGCGCCACCTGGTGTGCGCTGTTGCTGATGGTGCTGGCg                                                                                        >  2:619605/1‑104 (MQ=255)                                                                           ctGGTCGTCTGATGCATTATTACGGTTTTCATCACCGTCTGTTCCGCTGGCGACGCTCCGGCATGAGCGCCACCTGGTGTGCGCTGTTGCTGATGGTGCTGGCg                                                                                        <  1:619605/104‑1 (MQ=255)                                                                            tGGTCGTCTGATGCATTATTACGGTTTTCATCACCGTCTGTTCCGCTGGCGACGCTCCGGCATGAGCGCCACCTGGTGTGCGCTGTTGCTGATGGTGCTGGCGAATCTTTGGTATATGCCCTGGGAGTTGGTTTTCTcc                                                    >  1:1271820/1‑139 (MQ=255)                                                                              gtcgtcTGATGCATTATTACGGTTTTCATCACCGTCTGTTCCGCTGGCGACGTTCCGGCATGAGCGCCACCTGGTGTGCGCTGTTGCTGATGGTGCTGGCGAATCTTTGGTATATGCCCTGGGAGTTGGTTTTCTccc                                                   <  2:1117737/138‑1 (MQ=255)                                                                              gtcgtcTGATGCATTATTACGGTTTTCATCACCGTCTGTTCCGCTGGCGACGTTCCGGCATGAGCGCCACCTGGTGTGCGCTGTTGCTGATGGTGCTGGCGAATCTTTGGTATATGCCCTGGGAGTTGGTTTTCTccc                                                   <  2:1082589/138‑1 (MQ=255)                                                                                                      ttCATCACCGTCTGTTCCGCTGGCGACGTTCCGGCATGAGCGCCACCTGGTGTGCGCTGTTGCTGATGGTGCTGGCGAATCTTTGGTATATGCCCTGGGAGTTGGTTTTCTCCCTGCGTTAGCGCACAATACGCCActt                          >  2:1120567/1‑139 (MQ=255)                                                                                                      ttCATCACCGTCTGTTCCGCTGGCGACGCTCCGGCATGAgcgc                                                                                                                          >  2:474814/1‑43 (MQ=255)                                                                                                      ttCATCACCGTCTGTTCCGCTGGCGACGCTCCGGCATGAgcgc                                                                                                                          <  1:474814/43‑1 (MQ=255)                                                                                                      ttCATCACCGTCTGTTCCGCTGGCGACGCTCCGGCATGAGCGCCACCTGGTGTGCGCTGTTGCTGATGGTGCTGGCGAATCTTTGGTATATGCCCTGGGAGTTGGTTTTCTCCCTGCGTTAGCGCACAATACGCCActt                          >  1:229451/1‑139 (MQ=255)                                                                                                        catcaCCGTCTGTTCCGCTGGCGACGCTCCGGCATGAGCGCCACCTGGTGTGCGCTGTTGCTGATGGTGCTGGCGAATCTTTGGTATATGCCCTGGGAGTTGGTTTTCTCCCTGCGTTAGCGCACAATACGCCActttc                        >  1:241727/1‑139 (MQ=255)                                                                                                            aCCGTCTGTTCCGCTGGCGACGCTCCGGCATGAGCGCCACCTGGTGTGCGCTGTTGCTGATGGTGCTGGCGa                                                                                       <  2:1064957/72‑1 (MQ=255)                                                                                                            aCCGTCTGTTCCGCTGGCGACGCTCCGGCATGAGCGCCACCTGGTGTGCGCTGTTGCTGATGGTGCTGGCGa                                                                                       >  1:1064957/1‑72 (MQ=255)                                                                                                              cGTCTGTTCCGCTGGCGACGCTCCGGCATGAGCGCCACCTGGTGTGCGCTGTTGCTGATGGTGCTGGCGAATCTTTGGTATATGCCCTGGGAg                                                                <  2:13590/93‑1 (MQ=255)                                                                                                              cGTCTGTTCCGCTGGCGACGCTCCGGCATGAGCGCCACCTGGTGTGCGCTGTTGCTGATGGTGCTGGCGAATCTTTGGTATATGCCCTGGGAg                                                                >  1:13590/1‑93 (MQ=255)                                                                                                                tCTGTTCCGCTGGCGACGCTCCGGCATGAGCGCCACCTGGTGTgcg                                                                                                             >  1:1056021/1‑46 (MQ=255)                                                                                                                tCTGTTCCGCTGGCGACGCTCCGGCATGAGCGCCACCTGGTGTgcg                                                                                                             <  2:1056021/46‑1 (MQ=255)                                                                                                                tCTGTTCCGCTGGCGACGCTCCGGCATGAGCGCCACCTGGTGTGCGCTGTTGCTGATGGTGCTGGCGAATCTTTGGTATATGCCCTGGGAGTTGGTTTTCTCCCTGCGTTAGCGCACAATACGCCACTTTCTTTTTccc                >  2:789743/1‑139 (MQ=255)                                                                                                                tCTGTTCCGCTGGCGACGCTCCGGCATGAGCGCCACCTGGTGTGCGCTGTTGCTGATGGTGCTGGCGAATCTTTGGTATATGCCCTGGGAGTTGGTTTTCTCCCTGCGTTAGCGCACAATACGCCACTTTCTTTTTccc                >  1:834783/1‑139 (MQ=255)                                                                                                                    ttCCGCTGGCGACGTTCCGGCATGAGCGCCACCTGGTGTGCGCTGTTGCTGATGGTGCTGGCGAATCTTTGGTATATGCCCTGGGAGTTGGTTTTCTCCCTGCGTTAGCGCACAATACGCCACTTTCTTTTTCCCg               <  2:688885/136‑1 (MQ=255)                                                                                                                      ccGCTGGCGACGCTCCGGCATGAGCGCCACCTGGTGTGCGCTGTTGCTGATGGTGCTGGCGAATCTTTGGTATATGCCCTGGGAGTTGGTTTTCTCCCTGCGTTAGCGCACAATACGCCACTTTCTTTTTCCCGGAtt           <  1:1163407/138‑1 (MQ=255)                                                                                                                         cTGGCGACGCTCCGGCATGAGCGCCACCTGGTGTGCGCTGTTGCTGATGGTGCTGGCGAATCTTTGGTATATGCCCTGGGAGTTGGTTTTCTCCCTGCGTTAGCGca                                       >  2:590267/1‑107 (MQ=255)                                                                                                                         cTGGCGACGCTCCGGCATGAGCGCCACCTGGTGTGCGCTGTTGCTGATGGTGCTGGCGAATCTTTGGTATATGCCCTGGGAGTTGGTTTTCTCCCTGCGTTAGCGca                                       <  1:590267/107‑1 (MQ=255)                                                                                                                            gCGACGTTCCGGCATGAGCGCCACCTGGTGTGCGCTGTTGCTGATGGTGCTGGCGAATCTTTGGTATATGCCCTGGGAGTTGGTTTTCTCCCTGCGTTAGCGCACAATACGCCACTTTCTTTTTCCCGGATTTTTACg     <  2:20917/138‑1 (MQ=255)                                                                                                                              gACGCTCCGGCATGAGCGCCACCTGGTGTGCGCTGTTGCTGATGGTGCTGGCGAATCTTTGGTATATGCCCTGGGAGTTGGTTTTCTCCCTGCGTTAGCGCACAATACGCCACTTTCTTTTTCCCGGATTTTTACGTTa  >  1:1179317/1‑139 (MQ=255)                                                                                                                                  |                                                                                                                                       TGTGCTGATGCTGTTTATGGAAATGAATGGCGCAGAAACCTGGATGGTGCATATTTGCGGCATCGTTTTGCTTGCTGGTCGTCTGATGCATTATTACGGTTTTCATCACCGTCTGTTCCGCTGGCGACGTTCCGGCATGAGCGCCACCTGGTGTGCGCTGTTGCTGATGGTGCTGGCGAATCTTTGGTATATGCCCTGGGAGTTGGTTTTCTCCCTGCGTTAGCGCACAATACGCCACTTTCTTTTTCCCGGATTTTTACGTTA  >  NZ_CP009273/1946696‑1946959

Alignment Legend
Aligned base mismatch/match (shaded by quality score): ATCG/ATCG < 3 ≤ ATCG/ATCG < 16 ≤ ATCG/ATCG < 34 ≤ ATCG/ATCG < 38 ≤ ATCG/ATCG < 39 ≤ ATCG/ATCG
Unaligned base: atcg    Masked matching base: atcg    Alignment gap: ‑    Deleted base: ‑