Predicted mutation
evidence	seq id	position	mutation	freq	annotation	gene	description
RA	minE	313,477	T→C	7.9%	A204A (GCA→GCG)	acrA ←	multidrug efflux system

Read alignment evidence...
	seq id	position		ref	new	freq	score (cons/poly)	reads	annotation	genes	product
*	minE	313,477	0	T	C	7.9%	210.9 / 7.8	76	A204A (GCA→GCG)	acrA	multidrug efflux system
Reads supporting (aligned to +/- strand):  ref base T (32/38);  new base C (4/2);  total (36/40)
Fisher's exact test for biased strand distribution p-value = 4.14e-01
Kolmogorov-Smirnov test that lower quality scores support variant p-value = 9.80e-01

GTTTCAGGCGCAGGAAGTCGTTGCTGGACTGGGTCACATCAACGTAGATCGGATCAAGTTGCTGCACGGTTGCCAGCGCAGTCGCCTGACCGTTCTGTACCAATGCGCCTTCCGTCACGTTCGACTTACCAATGCGACCG  >  minE/313407‑313546                                                                       |                                                                      gTTTCAGGCGCAGGAAGTCGTTGCTGGACTGGGTCACATCAACGTAGATCGGATCAAGTTGCTGCACGGtt                                                                       >  1:1695547/1‑71 (MQ=255) gTTTCAGGCGCAGGAAGTCGTTGCTGGACTGGGTCACATCAACGTAGATCGGATCAAGTTGCTGCACGGtt                                                                       >  1:2545727/1‑71 (MQ=255)  tttCAGGCGCAGGAAGTCGTTGCTGGACTGGGTCACATCAACGTAGATCGGATCAAGTTGCTGCACGGTTg                                                                      >  1:3390775/1‑71 (MQ=255)   ttCAGGCGCAGGAAGTCGTTGCTGGACTGGGTCACATCAACGTAGATCGGATCAAGTTGCTGCACGGTTGc                                                                     >  1:975161/1‑71 (MQ=255)      aGGCGCAGGAAGTCGTTGCTGGACTGGGTCACATCAACGTAGATCGGATCAAGTTGCTGCACGGTTGCCAg                                                                  >  1:423130/1‑71 (MQ=255)      aGGCGCAGGAAGTCGTTGCTGGACTGGGTCACATCAACGTAGATCGGATCAAGTTGCTGCACGGTTGCCAg                                                                  <  1:3427590/71‑1 (MQ=255)      aGGCGCAGGAAGTCGTTGCTGGACTGGGTCACATCAACGTAGATCGGATCAAGTTGCTGCACGGTTGCCAg                                                                  <  1:3770735/71‑1 (MQ=255)          gcAGGAAGTCGTTGCTGGACTGGGTCACATCAACGTAGATCGGATCAAGTTGCTGCACGGTTGCCAGCGCa                                                              <  1:889669/71‑1 (MQ=255)          gcAGGAAGTCGTTGCTGGACTGGGTCACATCAACGTAGATCGGATCAAGTTGCTGCACGGTTGCCAGCGCa                                                              <  1:953390/71‑1 (MQ=255)           cAGGAAGTCGTTGCTGGACTGGGTCACATCAACGTAGATCGGATCAAGTTGCTGCACGGTTGCCAGCGCa                                                              <  1:2702468/70‑1 (MQ=255)           cAGGAAGTCGTTGCTGGACTGGGTCACATCAACGTAGATCGGATCAAGTTGCTGCACGGTTGCCAGCGCAg                                                             <  1:358370/71‑1 (MQ=255)             ggAAGTCGTTGCTGGACTGGGTCACATCAACGTAGATCGGATCAAGTTGCTGCACGGTTGCCAGCGCAGTc                                                           <  1:1496254/71‑1 (MQ=255)               aaGTCGTTGCTGGACTGGGTCACATCAACGTAGATCGGATCAAGTTGCTGCACGGTTGCCAGCGCAGTCGc                                                         <  1:3402261/71‑1 (MQ=255)                  tCGTTGCTGGATTGGGTCACATCAACGTAGATAGGATCGAGCTGCTGGACAGTCGcc                                                                    >  1:1482115/1‑57 (MQ=255)                    gTTGCTGGATTGGGTCACATCAACGTAGATAGGATCGAGCTGCTGGACAGTCGCCAgttc                                                               >  1:3406562/1‑57 (MQ=255)                    gTTGCTGGACTGGGTCACATCAACGTAGATCGGATCAAGTTGCTGCACGGTTGCCAGCGCAGTCGCCTg                                                      >  1:411650/1‑69 (MQ=255)                    gTTGCTGGACTGGGTCACATCAACGTAGATCGGATCAAGTTGCTGCACGGTTGCCAGCGCAGTCGCCTGAc                                                    >  1:788561/1‑71 (MQ=255)                     ttGCTGGACTGGGTCACATCAACGTAGATCGGATCAAGTTGCTGCACGGtt                                                                       >  1:2392360/1‑51 (MQ=255)                      tGCTGGACTGGGTCACATCAACGTAGATCGGATCAAGTTGCTGCACGGtt                                                                       >  1:3839957/1‑50 (MQ=255)                       gCTGGACTGGGTCACATCAACGTAGATCGGATCAAGTTGCTGCACGGTTGCCAGCGCAGTCGCCTGACCGt                                                 >  1:945334/1‑71 (MQ=255)                        cTGGATTGGGTCACATCAACGTAGATAGGATCGAGCTGCTGGACAGTCGCCAg                                                                  <  1:1871319/53‑1 (MQ=255)                        cTGGACTGGGTCACATCAACGTAGATCGGATCAAGTTGCTGCACGGTTGCCAGCGCAGTCGCCTGACCGtt                                                <  1:807792/71‑1 (MQ=255)                        cTGGACTGGGTCACATCAACGTAGATCGGATCAAGTTGCTGCACGGTTGCCAGCGCAGTCGCCTGACCGtt                                                <  1:3369820/71‑1 (MQ=255)                        cTGGACTGGGTCACATCAACGTAGATCGGATCAAGTTGCTGCACGGTTGCCAGCGCAGTCGCCTGACCGt                                                 <  1:1206319/70‑1 (MQ=255)                           gACTGGGTCACATCAACGTAGATCGGATCAAGTTGCTGCACGGTTGACAGCGCAGTCGCCTGACCGTTCTg                                             >  1:3455754/1‑71 (MQ=255)                            aCTGGGTCACATCAACGTAGATCGGATCAAGTTGCTGCACGGTTGCCAGCGCAGTCGCCTGACCGTTCTGt                                            <  1:2950033/71‑1 (MQ=255)                              tGGGTCACATCAACGTAGATCGGATCAAGTTGCTGCACGGTTGCCAGCGCAGTCGCCTGACCGTTCTGTAc                                          >  1:3263038/1‑71 (MQ=255)                                 gTCACATCAACGTAGATCGGATCAAGTTGCTGCACGGTTGcc                                                                    <  1:719810/42‑1 (MQ=255)                                   cacaTCAACGTAGATCGGATCAAGTTGCTGCACGGTTGCCAGCGCAGTCGCCTGACCGTTCTGTACCAATg                                     >  1:3279337/1‑71 (MQ=255)                                    acaTCAACGTAGATCGGATCAAGTTGCTGCACGGTTGCCAGCGCAGTCGCCTGACCGTTCTGTACCAATg                                     <  1:1604765/70‑1 (MQ=255)                                    acaTCAACGTAGATAGGATCGAGCTGCTGGACAGTCGCCAg                                                                  >  1:631459/1‑41 (MQ=255)                                    acaTCAACGTAGATAGGATCGAGCTGCTGGACAGTCGCCAGTTCAGTCgtt                                                        >  1:3892613/1‑49 (MQ=255)                                     caTCAACGTAGATCGGATCAAGTTGCTGCACGGTTGCCAGCGCAGTCGCCTGACCGTTCTGTACCAATgcg                                   >  1:541414/1‑71 (MQ=255)                                     caTCAACGTAGATAGGATCGAGCTGCTGGACAGTCGCCAg                                                                  <  1:2054337/40‑1 (MQ=255)                                      aTCAACGTAGATCGGATCAAGTTGCTGCACGGTTGCCAGCGCAGTCGCCTGACCGTTCTGTACCAATgcgc                                  >  1:3456739/1‑71 (MQ=255)                                       tCAACGTAGATCGGATCAAGTTGCTGCACGGTTGCCAGCGCAg                                                             >  1:2490898/1‑43 (MQ=255)                                       tCAACGTAGATCGGATCAAGTTGCTGCACGGTTGCCAGCGCAg                                                             >  1:167886/1‑43 (MQ=255)                                       tCAACGTAGATCGGATCAAGTTGCTGCACGGTTGCCAGCGCAGTc                                                           >  1:1134639/1‑45 (MQ=255)                                       tCAACGTAGATCGGATCAAGTTGCTGCACGGTTGCCAGCGCAGTCGCCTGACCGTTCTGTACCAATGCGcc                                 >  1:1457137/1‑71 (MQ=255)                                        cAACGTAGATCGGATCAAGTTGCTGCACGGTTGCCAGCGCAGTCGCCTGACCGTTCTGTACCAATgc                                    >  1:2738066/1‑67 (MQ=255)                                         aaCGTAGATCGGATCAAGTTGCTGCACGGTTGCCa                                                                   >  1:2041993/1‑35 (MQ=255)                                         aaCGTAGATCGGATCAAGTTGCTGCACGGTTGCCAGCGCAGTc                                                           <  1:2363394/43‑1 (MQ=255)                                         aaCGTAGATCGGATCAAGTTGCTGCACGGTTGCCAGCGCAGTCGCCTGACCGTTCTGTAc                                          >  1:3898596/1‑60 (MQ=255)                                             tAGATCGGATCAAGTTGCTGCACGGTTGCCAGCGCAGTCGCCTGACCGTTCTGTACCAATGCGCCTTCCg                            <  1:3299116/70‑1 (MQ=255)                                             tAGATCGGAT‑AAGTTGCTGCACGGTTGCCAGCGCAGTCGCCTGa                                                     >  1:3555581/1‑44 (MQ=38)                                              aGATCGGATCAAGTTGCTGCACGGTTGCCAGCGCAGTCGCCTGACCGTTCTGTACCAATGCGCCTTCCGt                           >  1:1079620/1‑70 (MQ=255)                                              aGATCGGATCAAGTTGCTGCACGGTTGCCAGCGCAGTCGCCTGACCGTTCTGTACCAATGCGCCTTCCGt                           >  1:1906485/1‑70 (MQ=255)                                                aTCGGATCAAGTTGCTGCACGGTTGCCAGCGCAGTCGCCTGACCGTTCTGTACCAATGCGCCTTCCGTCAc                        >  1:2066607/1‑71 (MQ=255)                                                 tCGGATCAAGTTGCTGCACGGTTGCCAGCGCAGTCGCCTGACCGTTCTGTACCa                                        <  1:2773043/54‑1 (MQ=255)                                                 tCGGATCAAGTTGCTGCACGGTTGCCAGCGCAGTCGCCTGACCGTTCTGTACCAATGCGCCTTCCGTCACg                       <  1:2235131/71‑1 (MQ=255)                                                   gtaTCAAGTTGCTGCACGGTTGCCAGCGCAGTCGCCTGACCGTTCTGTACCAATGCGCCTTCCGTCACGt                      <  1:2286188/68‑1 (MQ=255)                                                   ggATCAAGTTGCTGCACGGTTGCCAGCGCAGTCGCCTGACCGTTCTGTACCa                                        >  1:3383651/1‑52 (MQ=255)                                                   ggATCAAGTTGCTGCACGGTTGCCAGCGCAGTCGCCTGACCGTTCTGTACCAATGCGCCTTCCGTCACGt                      <  1:1272330/70‑1 (MQ=255)                                                    gATCAAGTTGCTGCACGGTTGCCAGCGCAGTCGCCTGACCGTTCTGTACCa                                        <  1:1804115/51‑1 (MQ=255)                                                    gATCAAGTTGCTGCACGGTTGCCAGCGCAGTCGCCTGACCGTTCTGTACCAATGCGCCTTCCGTCACGTTc                    <  1:2300564/71‑1 (MQ=255)                                                    gATCAAGTTGCTGCACGGTTGCCAGCGCAGTCGCCTGACCGTTCTGTACCAATGCGCCTTCCGTCACGTTc                    <  1:2190978/71‑1 (MQ=255)                                                    gATCAAGTTGCTGCACGGTTGCCAGCGCAGTCGCCTGACCGTTCTGTACCAATGCGCCTTCCGTCACGTTc                    <  1:1210534/71‑1 (MQ=255)                                                    gATCAAGTTGCTGCACGGTTGCCAGCGCAGTCGCCTGACCGTTCTGTACCAATGCGCCTTCCGTCACGTTc                    <  1:2933415/71‑1 (MQ=255)                                                     aTCAAGTTGCTGCACGGTTGCCAGCGCAGTCGCCTGACCGTTCTGTACCa                                        <  1:970748/50‑1 (MQ=255)                                                     aTCAAGTTGCTGCACGGTTGCCAGCGCAGTCGCCTGACCGTTCTGTACCAATGCGCCTTCCg                            <  1:2588989/62‑1 (MQ=255)                                                     aTCAAGTTGCTGCACGGTTGCCAGCGCAGTCGCCTGACCGTTCTGTACCAATGCGCCTTCCGTCACGTTc                    >  1:581912/1‑70 (MQ=255)                                                      tCAAGTTGCTGCACGGTTGCCAGCGCAGTCGCCTGACCGTTCTGTACCAATgc                                    <  1:1182810/53‑1 (MQ=255)                                                      tCAAGTTGCTGCACGGTTGCCAGCGCAGTCGCCTGACCGTTCTGTACCAATGCGCCTTCCGTCACGTTCGa                  >  1:629776/1‑71 (MQ=255)                                                      tCAAGTTGCTGCACGGTTGCCAGCGCAGTCGCCTGACCGTTCTGTACCAATGCGCCTTCCGTCACGTTCGa                  >  1:2853483/1‑71 (MQ=255)                                                       cAAGTTGCTGCACGGTTGCCAGCGCAGTCGCCTGACCGTTCTGTACCAATgcgc                                  <  1:1322249/54‑1 (MQ=255)                                                        aaGTTGCTGCACGGTTGCCAGCGCAGTCGCCTGACCGTTCTGTACCAATGCGCCTTCCGTCACGTTCGAc                 <  1:1353681/70‑1 (MQ=255)                                                         aGTTGCTGCACGGTTGCCAGCGCAGTCGCCTGACCGTTCTGTACCAATGCGcc                                 >  1:3416875/1‑53 (MQ=255)                                                         aGTTGCTGCACGGTTGCCAGCGCAGTCGCCTGACCGTTCTGTACCAATGCGCCTTCCGTCACGTTCGACtt               <  1:2862113/71‑1 (MQ=255)                                                         aGTTGCTGCACGGTTGCCAGCGCAGTCGCCTGACCGTTCTGTACCAATGCGCCTTCCGTCACGTTCGACtt               <  1:158687/71‑1 (MQ=255)                                                         aGTTGCTGCACGGTTGCCAGCGCAGTCGCCTGACCGTTCTGTACCAATGCGCCTTCCGTCACGTTCGACt                >  1:2719315/1‑70 (MQ=255)                                                             gctgcACGGTTGCCAGCGCAGTCGCCTGACCGTTCTGTACCAATGCGCCTTCCGTCACGTTCGACTTAcc            >  1:678621/1‑70 (MQ=255)                                                              ctgcACGGTTGCCAGCGCAGTCGCCTGACCGTTCTGTACCAATGCGCCTTCCGTCACGTTCGACTTACCa           <  1:289564/70‑1 (MQ=255)                                                                gcACGGTTGCCAGCGCAGTCGCCTGACCGTTCTGTACCAATGCGCCTTCCGTCACGTTCGACt                <  1:1958062/63‑1 (MQ=255)                                                                 cACGGTTGCCAGCGCAGTCGCCTGACCGTTCTGTACCAATGCGCCTTCCGTCACGtt                     >  1:1468650/1‑57 (MQ=255)                                                                 cACGGTTGCCAGCGCAGTCGCCTGACCGTTCTGTACCAATGCGCCTTCCGTCACGTTCGACTTACCAATGc       <  1:690335/71‑1 (MQ=255)                                                                  aCGGTTGCCAGCGCAGTCGCCTGACCGTTCTGTACCAATGCGCCTTCCGTCACGTTCGACTTACCAATGc       >  1:119929/1‑70 (MQ=255)                                                                   cGGTTGCCAGCGCAGTCGCCTGACCGTTCTGTACCAATGCGCCTTCCGTCACGTTCGACTTACCAATGCg      <  1:3711216/70‑1 (MQ=255)                                                                   cGGTTGCCAGCGCAGTCGCCTGACCGTTCTGTACCAATGCGCCTTCCGTCACGTTCGACTTACCAATGCGa     <  1:1682029/71‑1 (MQ=255)                                                                    ggTTGCCAGCGCAGTCGCCTGACCGTTCTGTACCAATGCGCCTTcc                             <  1:144312/46‑1 (MQ=255)                                                                    ggTTGCCAGCGCAGTCGCCTGACCGTTCTGTACCAATGCGCCTTCCGTCACGTTCGACTTACCAATGCGAc    >  1:80691/1‑71 (MQ=255)                                                                      ttGCCAGCGCAGTCGCCTGACCGTTCTGTACCAATGCGCCTTCCGTCACGTTCGACTTACCAATGCGACCg  >  1:3123756/1‑71 (MQ=255)                                                                       |                                                                      GTTTCAGGCGCAGGAAGTCGTTGCTGGACTGGGTCACATCAACGTAGATCGGATCAAGTTGCTGCACGGTTGCCAGCGCAGTCGCCTGACCGTTCTGTACCAATGCGCCTTCCGTCACGTTCGACTTACCAATGCGACCG  >  minE/313407‑313546

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: ‑