Predicted mutation
evidence	seq id	position	mutation	freq	annotation	gene	description
RA	minE	313,456	C→A	9.3%	P211P (CCG→CCT)	acrA ←	multidrug efflux system

Read alignment evidence...
	seq id	position		ref	new	freq	score (cons/poly)	reads	annotation	genes	product
*	minE	313,456	0	C	A	9.3%	237.1 / 6.7	75	P211P (CCG→CCT)	acrA	multidrug efflux system
Reads supporting (aligned to +/- strand):  ref base C (35/33);  new base A (5/2);  total (40/35)
Fisher's exact test for biased strand distribution p-value = 4.38e-01
Kolmogorov-Smirnov test that lower quality scores support variant p-value = 9.06e-01

TGCCATTCGCCAGTTCCTGTTTCAGGCGCAGGAAGTCGTTGCTGGACTGGGTCACATCAACGTAGATCGGATCAAGTTGCTGCACGGTTGCCAGCGCAGTCGCCTGACCGTTCTGTACCAATGCGCCTTCCGTCACG  >  minE/313389‑313525                                                                    |                                                                      tGCCATTCGCCAGTTCCTGTTTCAGGCGCAGGAAGTCGTTGCTGGACTGGGTCACATCAACGTAGATCGGa                                                                    <  1:3324538/71‑1 (MQ=255)      ttCGCCAGTTCCTGTTTCAGGCGCAGGAAGTCGTTGCTGGACTGGGTCACATCAACGTAGATCGGATCAAg                                                               >  1:1179310/1‑71 (MQ=255)      ttCGCCAGTTCCTGTTTCAGGCGCAGGAAGTCGTTGCTGGACTGGGTCACATCAACGTAGATCGGATCAAg                                                               >  1:3535527/1‑71 (MQ=255)      ttCGCCAGTTCCTGTTTCAGGCGCAGGAAGTCGTTGCTGGACTGGGTCACAT‑AACGTAGATCgg                                                                     <  1:3938030/64‑1 (MQ=255)        cGCCAGTTCCTGTTTCAGGCGCAGGAAGTCGTTGCTGGACTGGGTCACATCAACGTAGATCGGATCAAGt                                                              <  1:2771688/70‑1 (MQ=255)         gCCAGTTCCTGTTTCAGGCGCAGGAAGTCGTTGCTGGACTTGGTCACATCAACGTAGATCGGATCAAGTtg                                                            <  1:381997/71‑1 (MQ=255)             gTTCCTGTTTCAGGAGCAGGAAGTCGTTGCTGGACTGGGTCACATCAACGTAGATCGGATCAAGt                                                              <  1:2785126/65‑1 (MQ=255)              ttCCTGTTTCAGGCGCAGGAAGTCGTTGCTGGACTGGGTCACATCAACGTAGATCGGATc                                                                  <  1:2852124/60‑1 (MQ=255)              ttCCTGTTTCAGGCGCAGGAAGTCGTTGCTGGACTGGGTCACATCAACGTAGATCGGATCAAGTTGCTGCa                                                       >  1:2278772/1‑71 (MQ=255)                ccTGTTTCAGGCGCAGGAAGTCGTTGCTGGACTGGGTCACATCAACGTAGATCGGATCAAGTTGCTGCAc                                                      <  1:450876/70‑1 (MQ=255)                 cTGTTTCAGGCGCAGGAAGTCGTTGCTGGACTGGGTCACATCAACGTAGATCGGATCAAGTTGCTGCACgg                                                    <  1:2646348/71‑1 (MQ=255)                  tGTTTCAGGCGCAGGAAGTCGTTGCTGGACTGGGTCACATCAACGTAGATCGGATCAAGTtg                                                            >  1:2638386/1‑62 (MQ=255)                  tGTTTCAGGCGCAGGAAGTCGTTGCTGGACTGGGTCACATCAACGTAGATCGGATCAAGTtg                                                            >  1:3620079/1‑62 (MQ=255)                   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)                      tCAGGCGCAGGAAGTCGTTGCTGGACTGGGTCACATCAACGTAGATCGGATCAAGTtgctg                                                         >  1:2865771/1‑61 (MQ=255)                       cAGGCGCAGGAAGTCGTTGCTGGACTGGGTCACATCAACGTATATCGGATCAAGTTGCTGCACgg                                                    <  1:1447814/65‑1 (MQ=255)                        aGGCGCAGGAAGTCGTTGCTGGACTGGGTCACATCAACGTAGATCGGATCAAGTTGCTGCACGGTTGCCAg                                             <  1:3427590/71‑1 (MQ=255)                        aGGCGCAGGAAGTCGTTGCTGGACTGGGTCACATCAACGTAGATCGGATCAAGTTGCTGCACGGTTGCCAg                                             <  1:3770735/71‑1 (MQ=255)                        aGGCGCAGGAAGTCGTTGCTGGACTGGGTCACATCAACGTAGATCGGATCAAGTTGCTGCACGGTTGCCAg                                             >  1:423130/1‑71 (MQ=255)                            gcAGGAAGTCGTTGCTGGACTGGGTCACATCAACGTAGATCGGa                                                                    >  1:431604/1‑44 (MQ=255)                            gcAGGAAGTCGTTGCTGGACTGGGTCACATCAACGTAGATCGGATCAAGTTGCTGCACGGTTGCCAGCGCa                                         <  1:953390/71‑1 (MQ=255)                            gcAGGAAGTCGTTGCTGGACTGGGTCACATCAACGTAGATCGGATCAAGTTGCTGCACGGTTGCCAGCGCa                                         <  1:889669/71‑1 (MQ=255)                             cAGGAAGTCGTTGCTGGACTGGGTCACATCAACGTAGATCGGATCAAGTTGCTGCACGGTTGCCAGCGCa                                         <  1:2702468/70‑1 (MQ=255)                             cAGGAAGTCGTTGCTGGACTGGGTCACATCAACGTAGATCGGATCAAGTTGCTGCACGGTTGCCAGCGCAg                                        <  1:358370/71‑1 (MQ=255)                              aGGAAGTCGTTGCTGGACTGGGTCACATCAACGTAGATCGGATCAAGTTGCTGCACGGt                                                   <  1:2928788/59‑1 (MQ=255)                              aGGAAGTCGTTGCTGGACT‑GGTCACATCAACGTAGATCGGATCAAGTTGCTGCACGGt                                                   <  1:610422/58‑1 (MQ=255)                               ggAAGTCGTTGCTGGACTGGGTCACATCAACGTAGATCGGATCAAGTTGCTGCACGGTTGCCAGCGCAGTc                                      <  1:1496254/71‑1 (MQ=255)                                 aaGTCGTTGCTGGACTGGGTCACATCAACGTAGATCGGATCAAGTTGCTGCACGGTTGCCAGCGCAGTCGc                                    <  1:3402261/71‑1 (MQ=255)                                  aGTCGTTGCTGGACTGGGTCACATCAACGTAGATCGGATCAAGTtg                                                            >  1:3157123/1‑46 (MQ=255)                                    tCGTTGCTGGATTGGGTCACATCAACGTAGATAGGATCGAGCTGCTGGACAGTCGcc                                               >  1:1482115/1‑57 (MQ=255)                                    tCGTTGCTGGACTGGGTCACATCAACGTAGATCGGATCAAGTtg                                                            <  1:3384712/44‑1 (MQ=255)                                      gTTGCTGGATTGGGTCACATCAACGTAGATAGGATCGAGCTGCTGGACAGTCGCCAgttc                                          >  1:3406562/1‑57 (MQ=255)                                      gTTGCTGGACTGGGTCATATCAACGTAGATCGGATCAAGTTGCTGCACgg                                                    <  1:1763547/50‑1 (MQ=255)                                      gTTGCTGGACTGGGTCACATCAACGTAGATCGGATCAAGTTGCTGCACgg                                                    <  1:3638478/50‑1 (MQ=255)                                      gTTGCTGGACTGGGTCACATCAACGTAGATCGGATCAAGTTGCTGCACGGTTGCCAGCGCAGTCGCCTg                                 >  1:411650/1‑69 (MQ=255)                                      gTTGCTGGACTGGGTCACATCAACGTAGATCGGATCAAGTTGCTGCACGGTTGCCAGCGCAGTCGCCTGAc                               >  1:788561/1‑71 (MQ=255)                                       ttGCTGGACTGGGTCACATCAACGTAGATCGGATCAAGTTGCTGCACGGtt                                                  >  1:2392360/1‑51 (MQ=255)                                        tGCTGGACTGGGTCACATCAACGTAGATCGGATCAAGTTGCTGCa                                                       >  1:469065/1‑45 (MQ=255)                                        tGCTGGACTGGGTCACATCAACGTAGATCGGATCAAGTTGCTGCACGGtt                                                  >  1:3839957/1‑50 (MQ=255)                                         gCTGGACTGGGTCACATCAACGTAGATCGGATCAAGTTGCTGCa                                                       <  1:1756784/44‑1 (MQ=255)                                         gCTGGACTGGGTCACATCAACGTAGATCGGATCAAGTTGCTGCACGGTTGCCAGCGCAGTCGCCTGACCGt                            >  1:945334/1‑71 (MQ=255)                                          cTGGATTGGGTCACATCAACGTAGATAGGATCGAGCTGCTGGACAGTCGCCAg                                             <  1:1871319/53‑1 (MQ=255)                                          cTGGACTGGGTCACATCAACGTAGATCGGATCAAGTTGCTGCACGGTTGCCAGCGCAGTCGCCTGACCGtt                           <  1:3369820/71‑1 (MQ=255)                                          cTGGACTGGGTCACATCAACGTAGATCGGATCAAGTTGCTGCACGGTTGCCAGCGCAGTCGCCTGACCGtt                           <  1:807792/71‑1 (MQ=255)                                          cTGGACTGGGTCACATCAACGTAGATCGGATCAAGTTGCTGCACGGTTGCCAGCGCAGTCGCCTGACCGt                            <  1:1206319/70‑1 (MQ=255)                                             gACTGGGTCACATCAACGTAGATCGGATCAAGTTGCTGCACGGTTGACAGCGCAGTCGCCTGACCGTTCTg                        >  1:3455754/1‑71 (MQ=255)                                              aCTGGGTCACATCAACGTAGATCGGATCAAGTTGCTGCACGGTTGCCAGCGCAGTCGCCTGACCGTTCTGt                       <  1:2950033/71‑1 (MQ=255)                                               ttGGGTCACATCAACGTAGATAGGATCGAgctgct                                                          >  1:1358657/2‑35 (MQ=25)                                                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                                        >  1:167886/1‑43 (MQ=255)                                                         tCAACGTAGATCGGATCAAGTTGCTGCACGGTTGCCAGCGCAg                                        >  1:2490898/1‑43 (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      >  1:1906485/1‑70 (MQ=255)                                                                aGATCGGATCAAGTTGCTGCACGGTTGCCAGCGCAGTCGCCTGACCGTTCTGTACCAATGCGCCTTCCGt      >  1:1079620/1‑70 (MQ=255)                                                                  aTCGGATCAAGTTGCTGCACGGTTGCCAGCGCAGTCGCCTGACCGTTCTGTACCAATGCGCCTTCCGTCAc   >  1:2066607/1‑71 (MQ=255)                                                                   tCGGATCAAGTTGCTGCACGGTTGCCAGCGCAGTCGCCTGACCGTTCTGTACCa                   <  1:2773043/54‑1 (MQ=255)                                                                   tCGGATCAAGTTGCTGCACGGTTGCCAGCGCAGTCGCCTGACCGTTCTGTACCAATGCGCCTTCCGTCACg  <  1:2235131/71‑1 (MQ=255)                                                                    |                                                                      TGCCATTCGCCAGTTCCTGTTTCAGGCGCAGGAAGTCGTTGCTGGACTGGGTCACATCAACGTAGATCGGATCAAGTTGCTGCACGGTTGCCAGCGCAGTCGCCTGACCGTTCTGTACCAATGCGCCTTCCGTCACG  >  minE/313389‑313525

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: ‑