Read alignment evidence...
	seq id	position		ref	new	freq	score (cons/poly)	reads	annotation	genes	product
*	NC_000913	580,509	0	G	C	63.6%	41.0 / 75.4	66	L151L (CTG→CTC)	nohB	bacteriophage DNA packaging protein
Reads supporting (aligned to +/- strand):  ref base G (7/17);  new base C (18/24);  total (25/41)
Fisher's exact test for biased strand distribution p-value = 3.04e-01
Kolmogorov-Smirnov test that lower quality scores support variant p-value = 1.00e+00
Rejected as consensus: Frequency below/above cutoff threshold.

GGTGAAATTGCCAGTATTCTCGACGGGATCCCCCTGTCGGTGCAGCGGCGTTTTCCGGAACTGGAAAACCGACATGTTGATTTCCTGAAACGGGATATCATCAAAGCCATGAACAAAGCAGCCGCGCTGGATGAACTGATACCGGGGTTGCTGAGTGAATATATCGAACAGTCAGGTTA  >  NC_000913/580423‑580601                                                                                       |                                                                                             ggcgAAATTGCCAGTATTCTCGACGGGATCCCCCTGTCGGTGCAGCGGCGATTTCCGGAACTGGAAAACCGTCATGTTGATTTCCTGAAACgg                                                                                        >  1:500870/4‑93 (MQ=0)                              tcctcTGTCGGTTCAGCGGCGCTTCCCGGAGCTGGAAAACCGACATATTGATTTCCTCAAGAAGGACATCATTAAAGCCATGAACAAagcagc                                                           <  2:2933293/89‑1 (MQ=0)                              tcctcTGTCGGTTCAGCGGCGCTTCCCGGAGCTGGAAAACCGACATATTGATTTCCTCAAGAAGGACATCATTAAAGCCATGAACAAagcagc                                                           >  1:4050911/5‑93 (MQ=0)                              tcctcTGTCGGTTCAGCGGCGCTTCCCGGAGCTGGAAAACCGACATATTGATTTCCTCAAGAAGGACATCATTAAAGCCATGAACAAagcagc                                                           >  1:333428/5‑93 (MQ=0)                               cctcTGTCGGTTCAGCGGCGCTTCCCGGAGCTGGAAAACCGACATATTGATTTCCTCAAGAAGGACATCATTAAAGCCATGAACAAagcagct                                                          <  2:2552084/90‑2 (MQ=0)                               cctcTGTCGGTTCAGCGGCGCTTCCCGGAGCTGGAAAACCGACATATTGATTTCCTCAAGAAGGACATCATTAAAGCCATGAACAAagcagct                                                          <  2:2282805/90‑2 (MQ=0)                               cctcTGTCGGTTCAGCGGCGCTTCCCGGAGCTGGAAAACCGACATATTGATTTCCTCAAGAAGGACATCATTAAAGCCATGAACAAagcagct                                                          >  1:2977977/4‑92 (MQ=0)                                        gttcAGCGGCGCTTCCCGGAGCTGGAAAACCGACATATTGATTTCCTCAAGAAGGACATCATTAAAGCCATGAACAAAGCAGCTGCGCTGGag                                                 >  2:1282926/4‑92 (MQ=0)                                        gttcAGCGGCGCTTCCCGGAGCTGGAAAACCGACATATTGATTTCCTCAAGAAGGACATCATTAAAGCCATGAACAAAGCAGCTGCGCTGGAt                                                 >  2:321317/4‑93 (MQ=0)                                        gttcAGCGGCGCTTCCCGGAGCTGGAAAACCGACATATTGATTTCCTCAAGAAGGACATCATTAAAGCCATGAACAAAGCAGCTGCGCTGGAt                                                 >  2:2291077/4‑93 (MQ=0)                                        gttcAGCGGCGCTTCCCGGAGCTGGAAAACCGACATATTGATTTCCTCAAGAAGGACATCATTAAAGCCATGAACAAAGCAGCTGCGCTGGAt                                                 <  1:2196881/90‑1 (MQ=0)                                        gttcAGCGGAGCTTCCCGGAGCTGGAAAACCGACATATTGATTTCCTCAAGAAGGACATCATTAAAGCCATGAACAAAGCAGCTGCGCGGGAt                                                 <  2:759333/90‑1 (MQ=0)                                                   cttcccGGAGCTGGAAAACCGACATATTGATTTCCTCAAGAAGGACATCATTAAAGCCATGAACAAAGCAGCTGCGCTGGATGAAATAATAcc                                      >  2:925544/5‑93 (MQ=0)                                                   cttcccGGAGCTGGAAAACCGACATATTGATTTCCTCAAGAAGGACATCATTAAAGCCATGAACAAAGCAGCTGCGCTGGATGAAATAATAcc                                      >  1:3482658/5‑93 (MQ=0)                                                   cttcccGGAGCTGGAAAACCGACATATTGATTTCCTCAAGAAGGACATCATTAAAGCCATGAACAAAGCAGCTGCGCTGGATGAAATAATAcc                                      <  1:1570792/89‑1 (MQ=0)                                                    ttcccGGAGCTGGAAAACCGACATATTGATTTCCTCAAGAAGGACATCATTAAAGCCATGAACAAGGCAGCTGCGCTGGATGAAATAATACCg                                     <  2:2999860/90‑1 (MQ=0)                                                    ttcccGGAGCTGGAAAACCGACATATTGATTTCCTCAAGAAGGACATCATTAAAGCCATGAACAAAGCAGCTGCGCTGGATGAAATAATACCg                                     >  1:4002227/4‑93 (MQ=0)                                                    ttcccGGAGCTGGAAAACCGACATATTGATTTCCTCAAGAAGGACATCATTAAAGCCATGAACAAAGCAGCTGCGCTGGATGAAATAATACCg                                     <  2:4661590/90‑1 (MQ=0)                                                        cgtaaCTGGACAACCGACATGTTGATTTCCTGAAACGGGATATCATCAAAGCCATGAACAAAGCAGCCGCGCTGGATGAACTGATACCGGGGt                                 <  1:2739654/90‑1 (MQ=0)                                                          gagcTGGAAAACCGACATATTGATTTCCTCAAGAAGGACATCATTAAAGCCATGAACAAAGCAGCTGCGCTGGATGAAATAATACCGGGGTTg                               >  1:1144563/4‑93 (MQ=0)                                                                        aCATATTGATTTCCTCAAGAAGGACATCATTAAAGCCATGAACAAAGCAGCTGCGCTGGATGAAATAATACCGGGGTTGCTGAGTGAatatat                 >  2:226155/1‑93 (MQ=2)                                                                        aCATATTGATTTCCTCAAGAAGGACATCATTAAAGCCATGAACAAAGCAGCTGCGCTGGATGAAATAATACCGGGGTTGCTGAGTGAatatat                 >  1:2469466/1‑93 (MQ=11)                                                                         cATGTTGATTTCCTGAAACGGGATATCATCAAAGCCATGAACAAAGCAGCCGCGCTGGATGAACTGATACCGGGGTTGCTGAGTGAATATATc                <  1:2674474/93‑1 (MQ=32)                                                                         cATGTTGATTTCCTGAAACGGGATATCATCAAAGCCATGAACAAAGCAGCCGCGCTGGATGAACTGATACCGGGGTTGCTGAGTGAATATATc                >  2:18438/1‑93 (MQ=32)                                                                         cATCTTGATTTCCTGAAACGGGATATCATCAAAGCCATGAACAAAGCAGCCGCGCTGGATGAACTGATACCGGGGTTGCTGAGTGAATATATc                <  1:404541/93‑1 (MQ=17)                                                                         cATATTGATTTCCTCAAGAAGGACATCATTAAAGCCATGAACAAAGCAGCTGCGCTGGATGAAATAATACCGGGGTTGCTGAGTGAATATATc                <  2:4379842/93‑1 (MQ=11)                                                                         cATATTGATTTCCTCAAGAAGGACATCATTAAAGCCATGAACAAAGCAGCTGCGCTGGATGAAATAATACCGGGGTTGCTGAGTGAATATATc                <  1:730258/93‑1 (MQ=11)                                                                         cATATTGATTTCCTCAAGAAGGACATCATTAAAGCCATGAACAAAGCAGCGGCGCTGGATGAAATAATACCGGGGTTGCTGAGTGAATATATc                <  2:4067304/93‑1 (MQ=11)                                                                          atattGATTTCCTCAAGAAGGACATCATTAAAGCCATGAACAAAGCAGCTGCGCTGGATGAAATAATACCGGGGTTGCTGAGTGAATATATCg               >  1:2509127/4‑93 (MQ=2)                                                                           tattGATTTCCTCAAGAAGGACATCATTAAAGCCATGAACAAAGCAGCTGCGCTGGATGAAATAATACCGGGGTTGCTGAGTGAATATATCGa              >  1:4292024/3‑93 (MQ=11)                                                                           tattGATTTCCTCAAGAAGGACATCATTAAAGCCATGAACAAAGCAGCTGCGCTGGATGAAATAATACCGGGGTTGCTGAGTGAATATATCGa              >  1:1501567/3‑93 (MQ=11)                                                                           tGTTGATTTCCTGAAACGGGATATCATCAAAGCCATGAACAAAGCAGCCGCGCTGGATGAACTGATACCGGGGTTGCTGAGTGAATATATCGa              >  2:4083808/1‑93 (MQ=34)                                                                            gTTGATTTCCTGAAACGGGATATCATCAAAGCCATGAACAAAGCAGCCGCGCTGGATGAACTGATACCGGGGTTGCTGAGTGAATATATCGaa             >  2:4309817/1‑93 (MQ=35)                                                                            attGATTTCCTCAAGAAGGACATCATTAAAGCCATGAACAAAGCAGCTGCGCTGGATGAAATAATACCGGGGTTGCTGAGTGAATATATCGaa             <  2:1551988/92‑1 (MQ=11)                                                                            attGATTTCCTCAAGAAGGACATCATTAAAGCCATGAACAAAGCAGCTGCGCTGGATGAAATAATACCGGGGTTGCTGAGTGAATATATCGaa             <  2:1197894/92‑1 (MQ=11)                                                                            attGATTTCCTCAAGAAGGACATCATTAAAGCCATGAACAAAGCAGCTGCGCTGGATGAAATAATACCGGGGTTGCTGAGTGAATATATCGaa             <  2:128058/92‑1 (MQ=11)                                                                            attGATTTCCTCAAGAAGGACATCATTAAAGCCATGAACAAAGCAGCTGCGCTGGATGAAATAATACCGGGGTTGCTGAGTGAATATATCGaa             <  2:1551989/92‑1 (MQ=11)                                                                            attGATTTCCTCAAGAAGGACATCATTAAAGCCATGAACAAAGCAGCTGCGCTGGATGAAATAATACCGGGGTTGCTGAGTGAATATATCGaa             >  2:2901969/2‑93 (MQ=11)                                                                            attGATTTCCTCAAGAAGGACATCATTAAAGCCATGAACAAAGCAGCTGCGCTGGATGAAATAATACCGGGGTTGCTGAGTGAATATATCGaa             <  1:3093992/92‑1 (MQ=11)                                                                             ttGATTTCCTGAAACGGGATATCATCAAAGCCATGAACAAAGCAGCCGCGCTGGATGAACTGATACCGGGGTTGCTGAGTGAATCTATCGAAc            >  1:2001037/1‑93 (MQ=37)                                                                             ttGATTTCCTGAAACGGGATATCATCAAAGCCATGAACAAAGCAGCCGCGCTGGATGAACTGATACCGGGGTTGCTGAGTGAATATATCGAAc            <  2:828227/93‑1 (MQ=37)                                                                             ttGATTTCCTGAAACGGGATATCATCAAAGCCATGAACAAAGCAGCCGCGCTGGATGAACTGATACCGGGGTTGCTGAGTGAATATATCGAAc            >  1:295663/1‑93 (MQ=37)                                                                             ttGATTTCCTGAAACGGGATATCATCAAAGCCATGAACAAAGCAGCCGCGCTGGATGAACTGACACCGGGGTTGCTGAGTGAATATATCGAAc            <  2:828226/93‑1 (MQ=37)                                                                             ttGATTTCCTCAAGAAGGACATCATTAAAGCCATGAACAAAGCAGCTGCGCTGGATGAAATAATACCGGGGTTGCTGAGTGAATATATCGAAc            <  1:1593689/93‑1 (MQ=11)                                                                             ttGATTTCCTCAAGAAGGACATCATTAAAGCCATGAACAAAGCAGCTGCGCTGGATGAAATAATACCGGGGTTGCTGAGTGAATATATCGAAc            >  1:3751967/1‑93 (MQ=11)                                                                             ttGATTTCCTCAAGAAGGACATCATTAAAGCCATGAACAAAGCAGCTGCGCTGGATGAAATAATACCGGGGTTGCTGAGTGAATATATCGAAc            <  2:282318/93‑1 (MQ=11)                                                                              tGATTTCCTGAAACGGGATATCATCAAAGCCATGAACAAAGCAGCCGCGCTGGATGAACTGATACCGGGGTTGCTGAGTGAATATATCGAACa           <  2:4335638/93‑1 (MQ=38)                                                                              tGATTTCCTGAAACGGGATATCATCAAAGCCATGAACAAAGCAGCCGCGCTGGATGAACTGATACCGGGGTTGCTGAGTGAATATATCGAACa           <  1:1432258/93‑1 (MQ=38)                                                                              tGATTTCCTCAAGAAGGACATCATTAAAGCCATGAACAAAGCAGCTGCGCTGGATGAAATAATACCGGGGTTGCTGAGTGAATATATCGAACa           <  1:3785892/93‑1 (MQ=14)                                                                               gATTTCCTGAAACGGGATATCATCAAAGCCATGAACAAAGCAGCCGCGCTGGATGAACTGATACCGGGGTTGCTGAGTGAATATATCGAACAg          <  1:2075522/93‑1 (MQ=39)                                                                               gATTTCCTCAAGAAGGACATCATTAAAGCCATGAACAAAGCAGCTGCGCTGGATGAAATAATACCGGGGTTGCTGAGTGAATATATCGAACAg          <  1:4683364/93‑1 (MQ=14)                                                                                aTTTCCTGAAACGGGATATCATCAAAGCCATGAACAAAGCAGCCGCGCTGGATGAACTGATACCGGGGTTGCTGAGTGAATATATCGAACAgc         >  2:323924/1‑92 (MQ=39)                                                                                aTTTCCTGAAACGGGATATCATCAAAGCCATGAACAAAGCAGCCGCGCTGGATGAACTGATACCGGGGTTGCTGAGTGAATATATCGAACAGt         <  1:1209594/93‑1 (MQ=40)                                                                                aTTTCCTGAAACGGGATATCATCAAAGCCATGAACAAAGCAGCCGCGCTGGATGAACTGATACCGGGGTTGCTGAGTGAATATATCGAACAGt         <  1:3964565/93‑1 (MQ=40)                                                                                aTTTCCTCAAGAAGGACATCATTAAAGCCATGAACAAAGCAGCTGCGCTGGATGAAATAATACCGGGGTTGCTGAGTGAATATATCGAACAGt         <  1:1426429/93‑1 (MQ=14)                                                                                aTTTCCTCAAGAAGGACATCATTAAAGCCATGAACAAAGCAGCTGCGCTGGATGAAATAATACCGGGGTTGCTGAGTGAATATATCGAACAGt         >  1:906113/1‑93 (MQ=14)                                                                                aTTTCCTCAAGAAGGACATCATTAAAGCCATGAACAAAGCAGCTGCGCTGGATGAAATAATACCGGGGTTGCTGAGTGAATATATCGAACAGt         <  1:4012143/93‑1 (MQ=14)                                                                                aTTTCCTCAAGAAGGACATCATTAAAGCCATGAACAAAGCAGCTGCGCTGGATGAAATAATACCGGGGTTGCTGAGTGAATATATCGAACAGt         <  1:1426427/93‑1 (MQ=14)                                                                                aTTTCCTCAAGAAGGACATCATTAAAGCCATGAACAAAGCAGCTGCGCTGGATGAAATAATACCGGGGTTGCTGAGTGAATATATCGAACAGt         <  1:1463472/93‑1 (MQ=14)                                                                                 tttCCTGAAACGGGATATCATCAAAGCCATGAACAAAGCAGCCGCGCTGGATGAACTGATACCGGGGTTGCTGAGTGAATATATCGAACAGTc        >  1:2323373/1‑93 (MQ=255)                                                                                 tctCCTGAAACGGGATATCATCAAAGCCATGAACAAAGCAGCCGCGCTGGATGAACTGATACCGGGGTTGCTGAGTGAATATATCGAACAGTc        <  1:456141/91‑1 (MQ=255)                                                                                 gttCCTGAAACTGGATATCATCGAAGCCATGAACAGAGTAGCCGCGCTGGATGAACTGAGACCGGGGTTGCTGGGTGAATATATCGAACAGTc        <  1:2460764/92‑1 (MQ=14)                                                                                  ttCCTGAAACGGGATATCATCAAAGCCATGAACAAAGCAGCCGCGCTGGATGAACTGATACCGGGGTTGCTGAGTGAATATATCGAACAGTCa       <  1:1618732/93‑1 (MQ=255)                                                                                  ttCCTGAAACGGGATATCATCAAAGCCATGAACAAAGCAGCCGCGCTGGATGAACTGATACCGGGGTTGCTGAGTGAATATATCGAACAGTCa       <  2:4457553/93‑1 (MQ=255)                                                                                   tCCTGAAACGGGATATCATCAAAGCCATGAACAAAGCAGCCGCGCTGGATGAACTGATACCGGGGTTGCTGAGTGAATATATCGAACAGTCAg      <  2:1498313/93‑1 (MQ=255)                                                                                   tCCTGAAACGGGATATCATCAAAGCCATGAACAAAGCAGCCGCGCTGGATGAACTGATACCGGGGTTGCTGAGTGAATATATCGAACAGTCAg      <  2:603889/93‑1 (MQ=255)                                                                                    ccTGAAACGGGATATCATCAAAGCCATGAACAAAGCAGCCGCGCTGGATGAACTGATACCGGGGTTGCTGAGTGAATATATCGAACAGTCAgg     <  1:1487364/93‑1 (MQ=255)                                                                                     cTGAAACGGGATATCATCAAAGCCATGAACAAAGCAGCCGCGCTGGATGAACTGATACCGGGGTTGCTGAGTGAATATATCGAACAGTCAGGt    <  2:2966462/93‑1 (MQ=255)                                                                                      tGAAACGGGATATCATCAAAGCCATGAACAAAGCAGCCGCGCTGGATGAACTGATACCGGGGTTGCTGAGTGAATATATCGAACAGTCAGGtt   <  2:3197416/93‑1 (MQ=255)                                                                                      tGAAACGGGATATCATCAAAGCCATGAACAAAGCAGCCGCGCTGGATGAACTGATACCGGGGTTGCTGAGTGAATATATCGAACAGTCAGGtt   <  2:1943056/93‑1 (MQ=255)                                                                                       gAAACGGGATATCATCAAAGCCATGAACAAAGCAGCCGCGCTGGATGAACTGATACCGGGGTTGCTGAGTGAATATATCGAACAGTCAGGTTa  >  2:44533/1‑93 (MQ=255)                                                                                       |                                                                                             GGTGAAATTGCCAGTATTCTCGACGGGATCCCCCTGTCGGTGCAGCGGCGTTTTCCGGAACTGGAAAACCGACATGTTGATTTCCTGAAACGGGATATCATCAAAGCCATGAACAAAGCAGCCGCGCTGGATGAACTGATACCGGGGTTGCTGAGTGAATATATCGAACAGTCAGGTTA  >  NC_000913/580423‑580601

Alignment Legend
Aligned base mismatch/match (shaded by quality score): ATCG/ATCG < 3 ≤ ATCG/ATCG < 20 ≤ ATCG/ATCG < 29 ≤ ATCG/ATCG < 34 ≤ ATCG/ATCG < 41 ≤ ATCG/ATCG
Unaligned base: atcg    Masked matching base: atcg    Alignment gap: ‑    Deleted base: ‑