Predicted mutation
evidence	seq id	position	mutation	freq	annotation	gene	description
RA	minE	1,644,452	T→A	5.9%	M228L (ATG→TTG)	nlpB ←	lipoprotein

Read alignment evidence...
	seq id	position		ref	new	freq	score (cons/poly)	reads	annotation	genes	product
*	minE	1,644,452	0	T	A	5.9%	203.0 / 4.2	68	M228L (ATG→TTG)	nlpB	lipoprotein
Reads supporting (aligned to +/- strand):  ref base T (28/36);  new base A (2/2);  total (30/38)
Fisher's exact test for biased strand distribution p-value = 1.00e+00
Kolmogorov-Smirnov test that lower quality scores support variant p-value = 9.84e-01

CACATTGAACGGCCCGCGTACGACCAGCATTGGTAAACCGGTGTCATCAGCTGCACTTTGTACGTCCATAGTGGTGGAGGCACGATTTTGCGCAGCGTTCGCGGCGTCAGTGGCAGATTTATCCAGACCGGCGGAAAT  >  minE/1644384‑1644521                                                                     |                                                                      cacaTTGAACGGCCCGCGTACGACCAGCATTGGTAAACCGGTGTCATCAGCTGCACTATGGACGTACAAAg                                                                     <  1:2475901/71‑1 (MQ=255)  acaTTGAACGGCCCGCGTACGACCAGCATTGGTAAACCGGTGTCATCAGCTGCACTTTGTACGTCCATAgt                                                                    >  1:1096015/1‑71 (MQ=255)   caTTGAACGGCCCGCGTACGACCATCATTGGTAAACCGGTGTCATCAGCTGCACTTTGTACGTCCATAgtg                                                                   <  1:215284/71‑1 (MQ=255)   caTTGAACGGCCCGCGTACGACCAGCATTGGTAAACCGGTGTCATCAGCTGCACTTTGTACGTCCATAgtg                                                                   <  1:2276920/71‑1 (MQ=255)   caTTGAACGGCCCGCGTACGACCAGCATTGGTAAACCGGTGTCATCAGCTGCACTTTGTACGTCCATAgtg                                                                   <  1:974574/71‑1 (MQ=255)   caTTGAACGGCCCGCGTACGACCAGCATTGGTAAACCGGTGTCATCAGCTGCACTTTGTACGTCCATAgtg                                                                   <  1:282944/71‑1 (MQ=255)    aTTGAACGGCCCGCGTACGACCAGCATTGGTAAACCGGTGTCATCAGCTGCACTTTGTACGTCCATAgtgg                                                                  >  1:1307264/1‑71 (MQ=255)    aTTGAACGGCCCGCGTACGACCAGCATTGGTAAACCGGTGTCATCAGCTGCACTTTGTACGTCCATAgtgg                                                                  >  1:1348224/1‑71 (MQ=255)    aTTGAACGGCCCGCGTACGACCAGCATTGGTAAACCGGTGTCATCAGCTGCACTTTGTACGTCCATAgtg                                                                   >  1:972442/1‑70 (MQ=255)       gAACGGCCCGCGTACGACCAGCATTGGTAAACCGGTGTCATCAGCTGCACTTTGTACGTCCATAgtggtg                                                                <  1:2561662/70‑1 (MQ=255)        aaCGGCCCGCGTACGACCAGCATTGGTAAACCGGTGTCATCAGCTGCACTTTGTACGTCCATAgtggtg                                                                >  1:2880668/1‑69 (MQ=255)        aaCGGCCCGCGTACGACCAGCATTGGTAAACCGGTGTCATCAGCTGCACTTTGTACGTCCATAGtggtgg                                                               <  1:873049/70‑1 (MQ=255)        aaCGGCCCGCGTACGACCAGCATTGGTAAACCGGTGTCATCAGCTGCACTTTGTACGTCCATAGtggtgg                                                               <  1:772668/70‑1 (MQ=255)           ggCCCGCGTACGACCAGCATTGGTAAACCGGTGTCATCAGCTGCACTTTGTACGTCCATAGTGGTGGAGGc                                                           <  1:2122714/71‑1 (MQ=255)              ccGCGTACGACCAGCATTGTTAAACCGGTGTCATCAGCTGCACTTTGTACGTCCATAGTGGTGGAGGCACg                                                        <  1:123862/71‑1 (MQ=255)               cgcgTACGACCAGCATTGGTAAACCGGTGTCATCAGCTGCACTTTGTACGTCCATAGTGGTGGAGGCACGa                                                       <  1:1491880/71‑1 (MQ=255)               cgcgTACGACCAGCATTGGTAAACCGGTGTCATCAGCTGCACTTTGTACGTCCATAGTGGTGGAGGCACGa                                                       <  1:813563/71‑1 (MQ=255)               cgcgTACGACCAGCATTGGTAAACCGGTGTCATCAGCTGCACTTTGTACGTCCATAGTGGTGGAGGCACGa                                                       <  1:763239/71‑1 (MQ=255)               cgcgTACGACCAGCATTGGTAAACCGGTGTCATCAGCTGCACTTTGTACGTCCATAGTGGTGGAGGCACGa                                                       <  1:2490558/71‑1 (MQ=255)                 cgTACGACCAGCATTGGTAAACCGGTGTCATCAGCTGCACTTTGTACGTCCATAGTGGTGGAGGCACGAtt                                                     >  1:897294/1‑71 (MQ=255)                    aCGACCAGCATTGGTAAACCGGTGTCATCAGCTGCACTTTGTACGTCCATAGTGGTGGAGGCACGATTTTg                                                  >  1:2070982/1‑71 (MQ=255)                     cGACCAGCATTGGTAAACCGGTGTCATCAGCTGCACTTTGTACGTCCATAGTGGTGGAGGCACGATTTTgc                                                 >  1:1050543/1‑71 (MQ=255)                     cGACCAGCATTGGTAAACCGGTGTCATCAGCTGCACTTTGTACGTCCATAGTGGTGGAGGCACGATTTTgc                                                 >  1:2999412/1‑71 (MQ=255)                        ccAGCATTGGTAAACCGGTGTCATCAGCTGCACTTTGTACGTCCATAGTGGTGGAGGCACGATTTTGCGCa                                              <  1:26939/71‑1 (MQ=255)                           gCATTGGTAAACCGGTGTCATCAGCTGCACTATGGACGTACAAAg                                                                     <  1:2984836/45‑1 (MQ=25)                            cATTGGTAAACCGGTGTCATCAGCTGCACTTTGTACGTCCATAgtg                                                                   <  1:3031863/46‑1 (MQ=255)                             aTTGGTAAACCGGTGTCATCAGCTGCACTATGGACGTACAAAgtg                                                                   >  1:2844247/1‑45 (MQ=21)                             aTTGGTAAACCGGTGTCATCAGCTGCACTATGGACGTACAAAgtg                                                                   >  1:418479/1‑45 (MQ=21)                                ggTAAACCGGTGTCATCAGCTGCACTTTGTACGTCCATAgtgg                                                                  >  1:576944/1‑43 (MQ=255)                                ggTAAACCGGTGTCATCAGCTGCACTTTGTACGTCCATAgtgg                                                                  >  1:922105/1‑43 (MQ=255)                                ggTAAACCGGTGTCATCAGCTGCACTTTGTACGTCCATAgtgg                                                                  >  1:1092739/1‑43 (MQ=255)                                ggTAAACCGGTGTCATCAGCTGCACTTTGTACGTCCATAGTGGTGGAGGCACGATTTTGCGCAGCGTTcg                                       >  1:1415516/1‑70 (MQ=255)                                ggTAAACCGGTGTCATCAGCTGCACTTTGTACGTCCATAGTGGGGGAGGCACGATTTTGCGCAGCGTTcg                                       <  1:697026/70‑1 (MQ=255)                                 gTAAACCGGTGTCATCAGCTGCACTTTGTACGTCCATAgtggtg                                                                <  1:1300746/44‑1 (MQ=255)                                  tAAACCGGTGTCATCAGCTGCACTTTGTACGTCCATAgtggtg                                                                <  1:112498/43‑1 (MQ=255)                                   aaaCCGGTGTCATCAGCTGCACTTTGTACGTCCATAGTGGTGGa                                                              >  1:2216531/1‑44 (MQ=255)                                    aaCCGGTGTCATCAGCTGCACTTTGTACGTCCATAGTGGTGGa                                                              >  1:295652/1‑43 (MQ=255)                                          tgtCATCAGCTGCACTTTGTACGTCCATAGTGGTGGAGGCACGATTTTGCGCAGCGTTCGCGGCGTCAGTg                            <  1:2380876/71‑1 (MQ=255)                                           gtCATCAGCTGCACTTTGTACGTCCATAGTGGTGGAGGCACGATTTTGCGCAGCGTTCGCGGCGTCAGTgg                           >  1:2946515/1‑71 (MQ=255)                                              atcaGCTGCACTTTGTACGTCCATAGTGGTGGAGGCACGATTTTGCGCAGCGTTc                                        >  1:561064/1‑55 (MQ=255)                                              atcaGCTGCACTTTGTACGTCCATAGTGGTGGAGGCACGATTTTGCGCAGCGTTCGCGGCGTCAGTGGCAg                        <  1:2787568/71‑1 (MQ=255)                                                   cTGCACTTTGTACGTCCATAGTGGTGGAGGCACGATTTTGCGCAGCGTTCGCGGCGTCAGAGGCAGATTTa                   <  1:985194/71‑1 (MQ=255)                                                     gCACTTTGTACGTCCATAGTGGTGGAGGCACGATTTTGCGCAGCGTTCGCGGCGTCAGTGGCAGATTTATc                 >  1:2568991/1‑71 (MQ=255)                                                      cACTTTGTACGTCCATAGTGGTGGAGGCACGATTTTGCGCAGCGTTCGCGGCGTCAGTGGCAGATTTATcc                <  1:2946855/71‑1 (MQ=255)                                                      cACTTTGTACGTCCATAGTGGTGGAGGCACGATTTTGCGCAGCGTTCGCGGCGTCAGTGGCAGATTTATcc                <  1:1888968/71‑1 (MQ=255)                                                      cACTTTGTACGTCCATAGTGGTGGAGGCACGATTTTGCGCAGCGTTCGCGGCGTCAGTGGCAGATTTATc                 <  1:816481/70‑1 (MQ=255)                                                      cACTTTGTACGTCCATAGTGGTGGAGGCACGATTTTGCGCAGCGTTCGCGGCGTCAGTGGCAGATTTATc                 <  1:1106688/70‑1 (MQ=255)                                                       aCTTTGTACGTCCATAGTGGTGGAGGCACGATTTTGCGCAGCGTTCGCGGCGTCAGTGGCAGATTTATCCa               <  1:602418/71‑1 (MQ=255)                                                        cTTTGTACGTCCATAGTGGTGGAGGCACGATTTTGCGCAGCGTTCGCGGCGTCAGTGGCAGATTTATc                 >  1:989862/1‑68 (MQ=255)                                                        cTTTGTACGTCCATAGTGGTGGAGGCACGATTTTGCGCAGCGTTCGCGGCGTCAGTGGCAGATTTATCCAg              <  1:1655757/71‑1 (MQ=255)                                                         tttGTACGTCCATAGTGGTGGAGGCACGATTTTGCGCAGCGTTCGCGGCGTc                                <  1:3003637/52‑1 (MQ=255)                                                          ttGTACGTCCATAGTGGTGGAGGCACGATTTTGCGCAGc                                            >  1:2915630/1‑39 (MQ=255)                                                          ttGTACATCCATAGTGGTGGAGGCACGATTTTGCGCAGCGTTCGCGGCGTCAGTGGCAGATTTATCCAGAc            >  1:2474162/1‑71 (MQ=255)                                                           tGTACGTCCATAGTGGTGGAGGCACGATTTTGCGCAGCGTTCGCGGCGTCAGTGGCAGATTTATCCAGa             <  1:1972212/69‑1 (MQ=255)                                                           tGTACGTCCATAGTGGTGGAGGCACGATTTTGCGCAGCGTTCGCGGCGTCAGTGGCAGATTTATCCAGa             <  1:2697336/69‑1 (MQ=255)                                                           tGTACGTCCATAGTGGTGGAGGCACGATTTTGCGCAGCGTTCGCGGCGTCAGTGGCAGATTTATCCAGAcc           >  1:993025/1‑71 (MQ=255)                                                             tACGTCCATAGTGGTGGAGGCACGATTTTGCGCAGCGTTCGCGGCGGCAGTGGCAGATTTATCCAGACcg          <  1:2693183/70‑1 (MQ=255)                                                               cGTCCATAGTGGTGGAGGCACGATTTTGCGCAGCGTTCGCGGCGTCAGTGGCAGATTTATCCAGACcggcg       >  1:332003/1‑71 (MQ=255)                                                               cGTCCATAGTGGTGGAGGCACGATTTTGCGCAGCGTTCGCGGCGTCAGTGGCAGATTTATCCAGACcggcg       >  1:226504/1‑71 (MQ=255)                                                               cGTCCATAGTGGTGGAGGCACGATTTTGCGCAGCGTTCGCGGCGTCAGTGGCAGATTTATCCAGACcggcg       >  1:139358/1‑71 (MQ=255)                                                               cGTCCATAGTGGTGGAGGCACGATTTTGCGCAGCGTTCGCGGCGTCAGTGGCAGATTTATCCAGACcggc        <  1:2076791/70‑1 (MQ=255)                                                               cGTCCATAGTGGTGGAGGCACGATTTTGCGCAGCGTTCGCGGCGTCAGTGGCAGATTTATCCAGACcggc        <  1:2181509/70‑1 (MQ=255)                                                                 tCCATAGTGGTGGAGGCACGATTTTGCGCAGCGTTCGCGGCGTCAGTGGCAGATTTATCCAGACCGGCGGa     <  1:99675/71‑1 (MQ=255)                                                                   cATAGTGGTGGAGGCACGATTTTGCGCAGCGTTCGCGGCGTCAGt                             >  1:1678550/1‑45 (MQ=255)                                                                   cATAGTGGTGGAGGCACGATTTTGCGCAGCGTTCGCGGCGTCAGTGGCAGATTTAt                  >  1:800199/1‑56 (MQ=255)                                                                   cATAGTGGTGGAGGCACGATTTTGCGCAGCGTTCGCGGCGTCAGTGGCAGATTTAt                  >  1:23716/1‑56 (MQ=255)                                                                    aTAGTGGTGGAGGCACGATTTTGCGCAGCGTTCGCGGCGTCAGTGGCAGAttt                    <  1:2414687/53‑1 (MQ=255)                                                                    aTAGTGGTGGAGGCACGATTTTGCGCAGCGTTCGCGGCGTCAGTGGCAGATTTATCCAGACCGGCGGAAAt  <  1:2518573/71‑1 (MQ=255)                                                                     tAGTGGTGGAGGCACGATTTTGCGCAGCGTTCGCGGCGTCAGTGGCAGATTTATCCa               <  1:945578/57‑1 (MQ=255)                                                                     tAGTGGTGGAGGCACGATTTTGCGCAGCGTTCGCGGCGTCAGTGGCAGATTTATCCAGACCGGCGGAAAt  <  1:957693/70‑1 (MQ=255)                                                                     tAGTGGTGGAGGCACGATTTTGCGCAGCGTTCGCGGCGTCAGTGGCAGATTTATCCAGACCGGCGGAAAt  <  1:2640674/70‑1 (MQ=255)                                                                     |                                                                      CACATTGAACGGCCCGCGTACGACCAGCATTGGTAAACCGGTGTCATCAGCTGCACTTTGTACGTCCATAGTGGTGGAGGCACGATTTTGCGCAGCGTTCGCGGCGTCAGTGGCAGATTTATCCAGACCGGCGGAAAT  >  minE/1644384‑1644521

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: ‑