Predicted mutation
evidence	seq id	position	mutation	freq	annotation	gene	description
RA	minE	1,421,965	T→C	6.3%	L164L (CTA→CTG)	ccmF ←	heme lyase, CcmF subunit

Read alignment evidence...
	seq id	position		ref	new	freq	score (cons/poly)	reads	annotation	genes	product
*	minE	1,421,965	0	T	C	6.3%	166.8 / 3.1	63	L164L (CTA→CTG)	ccmF	heme lyase, CcmF subunit
Reads supporting (aligned to +/- strand):  ref base T (20/39);  new base C (2/2);  total (22/41)
Fisher's exact test for biased strand distribution p-value = 6.06e-01
Kolmogorov-Smirnov test that lower quality scores support variant p-value = 9.48e-01

CACCGAGAAACCCACGTACCCCATATAAAGCAGAGGCGGATGGAAGATCAGCCCCGGATCCTGCAATAGCGGGTTAAGATCGCGACCTTCAATCGGGAAGTTCGGCAACGTGCGAGAGAACGGGTTAGAGGTAAAG  >  minE/1421899‑1422034                                                                   |                                                                      cACCGAGAAACCCACGTACCCCATATAAAGCAGAGGCGGATGGAAGATCAGCCCCGGATCCTGCAATAGCg                                                                   <  1:2617290/71‑1 (MQ=255)     gagaAACCCACGTACCCCATATAAAGCAGAGGCCGATGGAAGATCAGCCCCGGATCCTGCAATAGCGGGt                                                                >  1:3840769/1‑70 (MQ=255)       gaAACCCACGTACCCCATATAAAGCAGAGGCGGATGGAAGATCAGCCCCGGATCCTGCAATAGCgc                                                                  >  1:1174800/1‑65 (MQ=255)       gaAACCCACGTACCCCATATAAAGCAGAGGCGGATGGAAGATCAGCCCCGGATCCTGCAATAGCGGGTTaa                                                             <  1:1556441/71‑1 (MQ=255)        aaaCCCACGTACCCCATATAAAGCAGAGGCGGATGGAAGATCAGCCCCGGATCCTGCAATAGCGGGTTAAg                                                            <  1:1375730/71‑1 (MQ=255)          aCCCACGTACCCCATATAAAGCAGAGGCGGATGGAAGATCAGCCCCGGATCCTGCAATAGCGGGTTAAGAt                                                          <  1:1490369/71‑1 (MQ=255)          aCCCACGTACCCCATATAAAGCAGAGGCGGATGGAAGATCAGCCCCGGATCCTGCAATAGCGGGTTAAGAt                                                          <  1:3444788/71‑1 (MQ=255)                 tACCCCATATAAAGCAGAGGCGGATGGAAGATCAGCCCCGGATCCTGCAACAGTGGGTTa                                                              <  1:2874820/60‑1 (MQ=255)                   ccccATATAAAGCAGAGGCGGATGGAAGATCAGCCCCGGATCCTGCAATAGCGGGTTAAGATCGCGACCtt                                                 <  1:3597909/71‑1 (MQ=255)                    cccATATAAAGCAGAGGCGGATGGAAGATCAGCCCCGGATCCTGCAATa                                                                      <  1:2364945/49‑1 (MQ=255)                     ccATATAAAGCAGAGGCGGATGGAAGATCAGCCCCGGATCCTGCAATAGCGGGTTAAGATcg                                                        >  1:2250262/1‑62 (MQ=255)                     ccATATAAAGCAGAGGCGGATGGAAGATCAGCCCCGGATCCTGCAATAGCGGGTTAAGATCGCGAcc                                                   <  1:1696886/67‑1 (MQ=255)                     ccATATAAAGCAGAGGCGGATGGAAGATCAGCCCCGGATCCTGCAATAGCGGGTTAAGATCGCGAc                                                    <  1:1155149/66‑1 (MQ=255)                      cATATAAAGCAGAGGCGGATGGAAGATCAGCCCCGGATCCTGCAATAGCGGGTTAAGATCGCGACCTTCaa                                              <  1:521641/71‑1 (MQ=255)                       atatAAAGCAGAGGCGGATGGAAGATCAGCCCCGGATCCTGCAATAGCGGGTTAAg                                                            <  1:4200204/56‑1 (MQ=255)                       atatAAAGCAGAGGCGGATGGAAGATCAGCCCCGGATCCTGCAATAGCGGGTTAAGa                                                           <  1:2271675/57‑1 (MQ=255)                        tataAATCAGAGGCGGATGGAAGATCAGCCCCGGATCCTGCAATat                                                                     <  1:1109863/46‑2 (MQ=255)                        tataAAGCAGAGGCGGATGGAAGATCAGCCCCGGATCCTGCAATAGCGGGtt                                                               <  1:312058/52‑1 (MQ=255)                        tataAAGCAGAGGCGGATGGAAGATCAGCCCCGGATCCTGCAATAGCGGGTTAAGATCGCGACCTTCAATc                                            <  1:4175596/71‑1 (MQ=255)                         ataAAGCAGAGGCGGATGGAAGATCAGCCCCGGATCCTGCAATAGCGGGTTAAGATCGCGACCTTCAATCg                                           >  1:1527851/1‑71 (MQ=255)                          taAAGCAGAGGCGGATGGAAGATCAGCCCCGGATCCTGCAATAGCGGGTTAAGATCGCGACCTTCAATc                                            >  1:2197769/1‑69 (MQ=255)                          taAAGCAGAGGCGGATGGAAGATCAGCCCCGGATCCTGCAATAGCGGGTTAAGATCGCGACCTTCAATCgg                                          >  1:1950210/1‑71 (MQ=255)                          taAAGCAGAGGCGGATGGAAGATCAGCCCCGGATCCTGCAATAGCGGGTTAAGATCGCGACCTTCAATCg                                           <  1:4470507/70‑1 (MQ=255)                          taAAGCAGAGGCGGATGGAAGATCAGCCCCGGATCATGCAATAGCGGGTTAAGATCGCGACCTTCAATCgg                                          >  1:1504416/1‑71 (MQ=255)                            aaGCAGAGGCGGATGGAAGATCAGCCCCGGATCCTGCAACAGTGGGTTAAGATCACGCCCTTCAATCGGGa                                        <  1:110618/71‑1 (MQ=255)                              gCAGAGGCGGATGGAAGATCAGCCCCGGATCCTGCAATAGCGGTTTAAGATcgc                                                       <  1:720494/54‑1 (MQ=255)                              gCAGAGGCGGATGGAAGATCAGCCCCGGATCCTGCAATAGCGGGTTAAGa                                                           >  1:3630223/1‑50 (MQ=255)                                    gCGGATGGAAGATCAGCCCCGGATCCTGCAATATCGGGTTAAGATCGCGACCTTCAATCGGGAAGTTCGGc                                <  1:2323918/71‑1 (MQ=255)                                    gCGGATGGAAGATCAGCCCCGGATCCTGCAATAGCGGGTTAAGATCGCGACCTTCAATCGGGAAGTTCGGc                                <  1:129131/71‑1 (MQ=255)                                      ggATGGAAGATCAGCCCCGGATCCTGCAATAGCGGGTTAAGATCGCGACCTTCAATCGGGAAGTTCGGCaa                              >  1:1095699/1‑71 (MQ=255)                                      ggATGGAAGATCAGCCCCGGATCCTGCAACAGTGGGTTAAGATCACGCCCTTCAATCGGGAAATTCGGCag                              >  1:3501241/1‑70 (MQ=255)                                      ggATGGAAGATCAGCCCCGGATCCTGCAACAGTGGGTTAAGATAACGCCCTTCAATCGGGAAATTCGGCag                              >  1:3777843/1‑70 (MQ=255)                                       gATGGAAGATCAGCCCCGGATCCTGCAATAGCGGGTTAAGATCGCGACCTTCAATCggg                                         <  1:2710327/59‑1 (MQ=255)                                        aTGGAAGATCAGCCCCGGATCCTGCAATAGCGGGTTAAGATCGCGACCTTCAATCGGGAAGTTCGGCAACg                            <  1:1846898/71‑1 (MQ=255)                                         tGGAAGATCAGCCCCGGATCCTGCAATAGCGGGTTAAGATCGCGACCTTCAATCGGGAAGTTCGGCAACGt                           >  1:807456/1‑71 (MQ=255)                                           gAAGATCAGCCCCGGATCCTGCAATAGCGGGTTAAGATCGCGAc                                                    >  1:2163388/1‑44 (MQ=255)                                           gAAGATCAGCCCCGGATCCTGCAATAGCGGGTTAAGATCGCGACCTTCAATCGGGAAGTTCGGCAACGt                           >  1:1983340/1‑69 (MQ=255)                                            aaGAGCAGCCCCGGAGCCTGCAATAGCGGGTTAAGATCGCTACCTTCAATCGGGAAGGTCGGCAACGTGCg                        <  1:2979957/71‑1 (MQ=255)                                             aGATCAGCCCCGGATCCTGCAATAGCGGGTTAAGATCGCGACCTTCAATCGGGAAGTTCg                                  >  1:1907142/1‑60 (MQ=255)                                             aGATCAGCCCCGGATCCTGCAATAGCGGGTTAAGATCGCGACCTTCAATCGGGAAGTTCGGCAACGTGCga                       <  1:3651497/71‑1 (MQ=255)                                              gATCAGCCCCGGATCCTGCAATAGCGGGTTAAGATcg                                                        <  1:2656467/37‑1 (MQ=255)                                              gATCAGCCCCGGATCCTGCAATAGCGGGTTAAGATCGCGACCTTCAATCGGGAAGTTCGGCAACGTGc                         <  1:3364582/68‑1 (MQ=255)                                              gATCAGCCCCGGATCCTGCAATAGCGGGTTAAGATCGCGACCTTCAATCGGGAAGTTCGGCAACGTGc                         <  1:1060759/68‑1 (MQ=255)                                              gATCAGCCCCGGATCCTGCAATAGCGGGTTAAGATCGCGACCTTCAATCGGGAAGTTCGGCAACGTGCgag                      <  1:3842619/71‑1 (MQ=255)                                               aTCAGCCCCGGATCCTGCAATAGCGGGTTAAGATCGCGACCTTCAATCGGGAAGTTCGGCAACGTg                          <  1:1763299/66‑1 (MQ=255)                                               aTCAGCCCCGGATCCTGCAATAGCGGGTTAAGATCGCGACCTTCAATCGGGAAGTTCGGCAACGTGCga                       >  1:3583813/1‑69 (MQ=255)                                                tCAGCCCCGGATCCTGCAATAGCGGGTTAAGATCGCGACCTTCAATCGGGAAGTTCGGCAACGTGCgagag                    <  1:2700669/71‑1 (MQ=255)                                                tCAGCCCCGGATCCTGCAATAGCGGGTTAAGATCGCGACCTTCAATCGGGAAGTTCGGCAACGTGCgagag                    <  1:73783/71‑1 (MQ=255)                                                tCAGCCCCGGATCCTGCAATAGCGGGTTAAGATCGCGACCTTCAATCGGGAAGTTCGGCAACGTGCgagag                    <  1:3602473/71‑1 (MQ=255)                                                 cAGCCCCGGATCCTGCAATAGCGGGTTAAGATCGCGACCTTCAATCGGGAAGTTCGGCAACGTGCgaga                     >  1:2388965/1‑69 (MQ=255)                                                 cAGCCCCGGATCATGCAATAGCGGGTTAAGATCGCGACCTTCAATCGGGa                                        >  1:739160/1‑50 (MQ=255)                                                    ccccGGATCCTGCAATAGCGGGTTAAGATCGCGACCTTCAATCGGGAAGTTCGGCAACGTGCGAGAGAACg                <  1:2688688/71‑1 (MQ=255)                                                         gATCCTGCAATAGCGGGTTAAGATCGCGACCTTCAATCGGGa                                        <  1:2625496/42‑1 (MQ=255)                                                         gATCCTGCAATAGCGGGTTAAGATCGCGACCTTCAATCGGGAAGTTCGGCAACGTGCgag                      <  1:2926917/60‑1 (MQ=255)                                                         gATCCTGCAATAGCGGGTTAAGATCGCGACCTTCAATCGGGAAGTTCGGCAACGTGCGAGAGAACggg              >  1:22067/1‑68 (MQ=255)                                                         gATCCTGCAATAGCGGGTTAAGATCGCGACCTTCAATCGGGAAGTTCGGCAACGTGCGAGAGAACGGGt             >  1:3149117/1‑69 (MQ=255)                                                         gATCCTGCAATAGCGGGTTAAGATCGCGACCTTCAATCGGGAAGTTCGGCAACGTGCGAGAGAACGGGt             >  1:483191/1‑69 (MQ=255)                                                          aTCCTGCAATAGCGGGTTAAGATCGCGACCTTCAATCGGGAAGTTCGGCAACGTGCGAGAGAACGGGTTag          <  1:426034/71‑1 (MQ=255)                                                          aTCCTGCAATAGCGGGTTAAGATCGCGACCTTCAATCGGGAAGTTCGGCAACGTGCGAGAGAACGGGTTag          <  1:933947/71‑1 (MQ=255)                                                           tCCTGCAATAGCGGGTTAAGATCGCGACCTTCAATCGGGAAGTTCGGCAACGTGCGAGAGAACGGGTTaga         <  1:3127737/71‑1 (MQ=255)                                                              tGCAATAGCGGGTTAAGATCGCGACCTTCAATCggg                                         <  1:2760493/36‑1 (MQ=255)                                                               gCAATAGCGGGTTAAGATCGCGACCTTCAATCGGGAAGTTCGGCAACGTGCGAGAGAACGGGTTAGAGGt      >  1:4574115/1‑70 (MQ=255)                                                                  aTAGCGGGTTAAGATCGCGACCTTCAATCGGGAAGTTCGGCAACGTGCGAGAGAACGGGTTAGAGGTAAag  <  1:2348358/71‑1 (MQ=255)                                                                   tAGCGGGTTAAGATCGCGACCTTCAATCGGGAAGTTCGGCAACGTGCGAGAGaa                  <  1:294102/54‑1 (MQ=255)                                                                   tAGCGGGTTAAGATCGCGACCTTCAATCGGGAAGTTCGGCAACGTGCGAGAGAACGGGTTAGAGGTaaa   >  1:2606226/1‑69 (MQ=255)                                                                   |                                                                      CACCGAGAAACCCACGTACCCCATATAAAGCAGAGGCGGATGGAAGATCAGCCCCGGATCCTGCAATAGCGGGTTAAGATCGCGACCTTCAATCGGGAAGTTCGGCAACGTGCGAGAGAACGGGTTAGAGGTAAAG  >  minE/1421899‑1422034

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: ‑