Predicted mutation
evidence	seq id	position	mutation	freq	annotation	gene	description
RA	NC_002947	4,318,829	G→T	8.2%	G364* (GGA→TGA)	PP_3789 →	efflux transporter

Read alignment evidence...
	seq id	position		ref	new	freq	score (cons/poly)	reads	annotation	genes	product
*	NC_002947	4,318,829	0	G	T	8.2%	138.7 / 3.9	50	G364* (GGA→TGA)	PP_3789	efflux transporter
Reads supporting (aligned to +/- strand):  ref base G (20/24);  new base T (2/2);  total (23/27)
Fisher's exact test for biased strand distribution p-value = 1.00e+00
Kolmogorov-Smirnov test that lower quality scores support variant p-value = 5.80e-01

TGCTAGTTTTCACCCTTGGCGAGCTGCTGATTCAGCCAGCGGAGTATCTCTACATTGACTCGATCAGCCCGCCGCCCCTCAAAGGCAGTTATTTCGCCGCACACAATCTGGCGAGCTTGGGGGCGGCAGTCAGCCCGGCGTGGTGTGGATTCA‑‑‑TACTATCGCTCG‑CGGGCCCCCAGGGTTTGTGCTTCTCACTGATCGCCTGCGTGCTGGCGGGTAGCAGCCTTTGTGCCATGCGCCCTCGACTGACCCCGGGCAACTTTGCGCGGGGAGATCTTTAAT  >  NC_002947/4318683‑4318961                                                                                                                                                   |                                                                                                                                         tGCTAGTTTTCACCCTTGGCGAGCTGCTGATTCAGCCAGCGGAGTATCTCTACATTGACTCGATCAGCCCGCCGCCCCTCAAAGGCAGTTATTTCGCCGCACACAATCTGGCGAGCTTGGGGGCGGCAGTCAGCCCGGCGTGGTGTGGa                                                                                                                                        <  1:80029/149‑1 (MQ=255)    tAGTTTTCACCCTTGGCGAGCTGCTGATTCAGCCAGCGGAGTATCTCTACATTGACTCGATCAGCCCGCCGCCCCTCAAAGGCAGTTATTTCGCCGCACACAATCTGGCGAGCTTGGGGGCGGCAGTCAGCCCGGCGTGGTGTTGAtt                                                                                                                                      >  1:110678/1‑148 (MQ=255)    tAGTTTTCACCCTTGGCGAGCTGCTGATTCAGCCAGCGGAGTATCTCTACATTGACTCGATCAGCCCGCCGCCCCTCAAAGGCAGTTATTTCGCCGCACACAATCTGGCGAGCTTGGGGGCGGCAGTCAGCCCGGCGTGGTGTTGAtt                                                                                                                                      >  1:106425/1‑148 (MQ=255)    tAGTTTTCACCCTTGGCGAGCTGCTGATTCAGCCAGCGGAGTATCTCTACATTGACTCGATCAGCCCGCCGCCCCTCAAAGGCAGTTATTTCGCCGCACACAATCTGGCGAGCTTGGGGGCGGCAGTCAGCCCGGCGTGGTGTGGAtt                                                                                                                                      >  8:8035/1‑148 (MQ=255)    tAGTTTTCACCCTTGGCGAGCTGCTGATTCAGCCAGCGGAGTATCTCTACATTGACTCGATCAGCCCGCCGCCCCTCAAAGGCAGTTATTTCGCCGCACACAATCTGGCGAGCTTGGGGGCGGCAGTCAGCCCGGCGTGGTGTGGAtt                                                                                                                                      >  7:94977/1‑148 (MQ=255)      gTTTTCACCCTTGGCGAGCTGCTGATTCAGCCAGCGGAGTATCTCTACATTGACTCGATCAGCCCGCCGCCCCTCAAAGGCAGTTATTTCGCCGCACACAATCTGGCGAGCTTGGGGGCGGCAGTCAGCCCGGCGTGGTGTGGATTc                                                                                                                                     <  3:17588/147‑1 (MQ=255)      gTTTTCACCCTTGGCGAGCTGCTGATTCAGCCAGCGGAGTATCTCTACATTGACTCGATCAGCCCGCCGCCCCTCAAAGGCAGTTATTTCGCCGCACACAATCTGGCGAGCTTGGGGGCGGCAGTCAGCCCGGCGTGGTGTGGATTCa                                                                                                                                    <  7:290863/148‑1 (MQ=255)      gTTTTCACCCTTGGCGAGCTGCTGATTCAGCCAGCGGAGTATCTCTACATTGACTCGATCAGCCCGCCGCCACTCAAACTCAGTTATTTCGCCGCACACAATCTGGCGAGCTTGGGTGCGGCAGTCAGCCCGGCGTGGTGTGGATTc                                                                                                                                     <  5:161824/147‑1 (MQ=255)              ccTTGGCGAGCTGCTGATTCAGCCAGCGGAGTATCTCTACATTGACTCGATCAGCCCGCCGCCCCTCAAAGGCAGTTATTTCGCCGCACACAATCTGGCGAGCTTGGGGGCGGCAGTCAGCCCGGCGTGGTGTGGATTCA‑‑‑TACTAtcgc                                                                                                                        >  4:177239/1‑149 (MQ=255)                          gctgATTCAGCCAGCGGAGTATCTCTACATTGACTCGATCAGCCCGCCGCCCCTCAAAGGCAGTTATTTCGCCGCACACAATCTGGCGAGCTTGGGGGCGGCAGTCAGCCCGGCGTGGTGTGGATTCA‑‑‑TACTATCGCTCG‑CGGGcccc                                                                                                            >  3:3296/1‑148 (MQ=255)                                tCAGCCAGCGGAGTATCTCTACATTGACTAGATCAGCCCGCCGCCCCTCAAAGGCAGTTATTTCGCCGCACACAATCTGGCGAGCTTGGGGGCGGCAGTCAGCCCGGCGTGGTGTGGATTCA‑‑‑TACTATCGCTCG‑CGGGCCCCCAGGGtt                                                                                                     >  6:284422/1‑149 (MQ=255)                                  agccagcGGAGTATCTCTACATTGACTCGATCAGCCCGCCGCCCCTCAAAGGCAGTTATTTCGCCGCACACAATCTGGCGAGCTTGGGGGCGGCAGTCAGCCCGGCGTGGTGTGGATTCA‑‑‑TACTATCGCTCG‑CGGGCCCCCAGGGttt                                                                                                    <  7:8035/148‑1 (MQ=255)                                   gccagcGGAGTATCTCTACATTGACTCGATCAGCCCGCCGCCCCTCAAAGGCAGTTATTTCGCCGCACACAATCTGGCGAGCTTGGGGGCGGCAGTCAGCCCGGCGTGGTGTGGATTCA‑‑‑TACTATCGCTCG‑CGGGCCCCCAGGGTTtgt                                                                                                  >  8:151656/1‑149 (MQ=255)                                    ccagcGGAGTATCTCTACATTGACTCGATCAGCCCGCCGCCCCTCAAAGGCAGTTATTTCGCCGCACACAATCTGGCGAGCTTGGGGGCGGCAGTCAGCCCGGCGTGGTGTGGATTCA‑‑‑TACTATCGCTCG‑CGGGCCCCCAGGGTTtgtg                                                                                                 >  5:133065/1‑149 (MQ=255)                                      agcGGAGTATCTCTACATTGACTCGATCAGCCCGCCGCCCCTCAAAGGCAGTTATTTCGCCGCACACAATCTGGCGAGCTTGGGGGCGGCAGTCAGCCCGGCGTGGTGTGGATTCA‑‑‑TACTATCGCTCG‑CGGGCCCCCAGGGTTTGTGCt                                                                                               >  5:192019/1‑149 (MQ=255)                                       gcGGAGTATCTCTACATTGACTCGATCAGCCCGCCGCCCCTCAAAGGCAGTTATTTCGCCGCACACAATCTGGCGAGCTTGGGGGCGGCAGTCAGCCCGGCGTGGTGTTGATTCA‑‑‑TACTATCGCTCG‑CGGGCCCCCAGGGTTTGTGCtt                                                                                              <  2:106425/149‑1 (MQ=255)                                       gcGGAGTATCTCTACATTGACTCGATCAGCCCGCCGCCCCTCAAAGGCAGTTATTTCGCCGCACACAATCTGGCGAGCTTGGGGGCGGCAGTCAGCCCGGCGTGGTGTTGATTCA‑‑‑TACTATCGCTCG‑CGGGCCCCCAGGGTTTGTGCtt                                                                                              <  2:110678/149‑1 (MQ=255)                                        cGGAGTATCTCTAGATTGTCTCGATCAGCCCGCCGCCGCTCTCAGGGAGTTATTTCGCCGCTCACAATCTGGCGAGCTTGGGGGCGGCTGTCAGCCCGGCGTGGTGTGGTTTCA‑‑‑TACTATCGCTCG‑CGGGCCCCCAGGGTTTGTGCTtc                                                                                             <  4:158517/149‑1 (MQ=255)                                           aGTATCTCTACATTGACTCGATCAGCCCGCCGCCCCTCAAAGGCAGTTATTTCGCCGCACACAATCTGGCGAGCTTGGGGGCGGCAGTCAGCCCGGCGTGGTGTGGATTCA‑‑‑TACTATCGCTCG‑CGGGCCCCCAGGGTTTGTGCTTCTCa                                                                                          <  2:183755/149‑1 (MQ=255)                                             tATCTCTACATTGACTCGATCAGCCCGCCGCCCCTCAAAGGCAGTTATTTCGCCGCACACAATCTGGCGAGCTTGGGGGCGGCAGTCAGCCCGGCGTGGTGTGGATTCA‑‑‑TACTATCGCTCGCCGGGCCCCCAGGGTTTGTGCTTCTCa                                                                                          <  1:5305/148‑1 (MQ=255)                                              aTCTCTACATTGACTCGATCAGCCCGCCGCCCCTCAAAGGCAGTTATTTCGCCGCACACAATCTGGCGAGCTTGGGGGCGGCAGTCAGCCCGGCGTGGTGTGGATTCA‑‑‑TACTATCGCTCG‑CGGGCCCCCAGGGTTTGTGCTTCTCACt                                                                                        <  4:3296/148‑1 (MQ=255)                                               tctcTACATTGACTCGATCAGCCCGCCGCCCCTCAAAGGCAGTTATTTCGCCGCACACAATCTGGCGAGCTTGGGGGCGGCAGTCAGCCCGGCGTGGTGTGGATTCA‑‑‑TACTATCGCTCG‑CGGGCCCCCAGGGTTTGTGCTTATCACTGa                                                                                      >  5:357228/1‑149 (MQ=255)                                                ctctACATTGACTCGATCAGCCCGCCGCCCCTCAAAGGCAGTTATTTCGCCGCACACAATCTGGCGAGCTTGGGGGCGGCAGTCAGCCCGGCGTGGTGTGGATTCA‑‑‑TACTATCGCTCG‑CGGGCCCCCAGGGTTTGTGCTTCTCACTGAt                                                                                     >  5:225204/1‑149 (MQ=255)                                                       ttGACTCGATCAGCCCGCCGCCCCTCAAAGGCAGTTATTTCGCCGCACACAATCTGGCGAGCTTGGGGGCGGCAGTCAGCCCGGCGTGGTGTGGATTCA‑‑‑TACTATCGCTCG‑CGGGCCCCCAGGGTTTGTGCTTCTCACTGATCGCCTGc                                                                              <  5:284422/149‑1 (MQ=255)                                                            tCGATCAGCCCGCCGCCCCTCAAAGGCAGTTATTTCGCCGCACACAATCTGGCGAGCTTGGGGGCGGCAGTCAGCCCGGCGTGGTGTGGATTCA‑‑‑TACTATCGCTCG‑CGGGCCCCCAGGGTTTGTGCTTCTCACTGATCGCCTGCGTGCt                                                                         >  1:173341/1‑149 (MQ=255)                                                               aTCAGCCCGCCGCCCCTCAAAGGCAGTTATTTCGCCGCACACAATCTGGCGAGCTTGGGGGCGGCAGTCAGCCCGGCGTGGTGTGGATTCA‑‑‑TACTATCGCTCG‑CGGGCCCCCAGGGTTTGTGCTTCTCACTGATCGCCTGCGTGCTGGc                                                                      <  6:357228/149‑1 (MQ=255)                                                               aTCAGCCCGCCGCCCCTCAAAGGCAGGTATTTCGCCGCACACAATCTGGCGAGCTTGGGGGCGGCAGTCAGCCCGGCGTGGTGTGGATTCA‑‑‑TACTATCGCTCG‑CGGGCCCCCAGGGTTTGTGCTTCTCACTGATCGCCTGCGTGCTGGc                                                                      <  8:94977/149‑1 (MQ=255)                                                                  aGCCCGCCGCCCCTCAAAGGCAGTTATTTCGCCGCACACAATCTGGCGAGCTTGGGGGCGGCAGTCAGCCCGGCGTGGTGTGGATTCA‑‑‑TACTATCGCTCG‑CGGGCCCCCAGGGTTTGTGCTTCTCACTGATCGCCTGCGTGCTGGCgg                                                                    <  1:151318/148‑1 (MQ=255)                                                                   gCCCGCCGCCCCTCAAAGGCAGTTATTTCGCCGCACACAATCTGGCGAGCTTGGGGGCGGCAGTCAGCCCGGCGTGGTGTAGATTCA‑‑‑TACTATCGCTCG‑CGGGCCCCCAGGGTTTGTGCTTCTCAc                                                                                         <  6:253913/126‑1 (MQ=255)                                                                   gCCCGCCGCCCCTCAAAGGCAGTTATTTCGCCGCACACAATCTGGCGAGCTTGGGGGCGGCAGTCAGCCCGGCGTGGTGTAGATTCA‑‑‑TACTATCGCTCG‑CGGGCCCCCAGGGTTTGTGCTTCTCAc                                                                                         >  5:253913/1‑126 (MQ=255)                                                                    cccGCCGCCCCTCAAAGGCAGTTATTTCGCCGCACACAATCTGGCGAGCTTGGGGGCGGCAGTCAGCCCGGCGTGGTGTGGATTCA‑‑‑TACTATCGCTCG‑CGGGCCCCCAGGGTTTGTGc                                                                                                >  5:32882/1‑118 (MQ=255)                                                                    cccGCCGCCCCTCAAAGGCAGTTATTTCGCCGCACACAATCTGGCGAGCTTGGGGGCGGCAGTCAGCCCGGCGTGGTGTGGATTCA‑‑‑TACTATCGCTCG‑CGGGCCCCCAGGGTTTGTGc                                                                                                <  6:32882/118‑1 (MQ=255)                                                                            cccTCAAAGGCAGTTATTTCGCCGCACACAATCTGGCGAGCTTGGGGGCGGCAGTCAGCCCGGCGTGGTGTGGATTCA‑‑‑TACTATCGCTCG‑CGGGCCCCCAGGGTTTGTGCTTCTCACTGATCGCCTGCGTGCTGGCGGGTAGCAGCCtt                                                         >  7:120509/1‑149 (MQ=255)                                                                                 aaaGGCAGTTATTTCGCCGCACACAATCTGGCGAGCTTGGGGGCGGCAGTCAGCCCGGCGTGGTGTGGATTCA‑‑‑TACTATCGCTCG‑CGGGCCCCCAGGGTTTGTGCTTCTCACTGATCGCCTGCGTGCTGGCGGGTAGCAGCCTTtgt                                                      <  6:225204/147‑1 (MQ=255)                                                                                   acgCAGTTATTTCGCCGCACACAATCTGGCGAGCTTGGGGGCGGCAGGCAGCCCGGCGGGGTGTGGATTCA‑‑‑TACTATCGCTCG‑CGGGCCCCCAGGGTTTGTGCGTCTCACTGATCGCCTGCGTGCTGGCGGGTAGCAGCCTTtgt                                                      <  8:273034/143‑1 (MQ=255)                                                                                   aGGCAGTTATTTCGCCGCACACAATCTGGCGAGCTTGGGGGCGGCAGTCAGCCCGGCGTGGTGTGGATTCA‑‑‑TACTATCGCTCG‑CGGGCCCCCAGGGTTTGTGCTTCTCACTGATCGCCTGCGTGCTGGCGGGTAGCAGCCTTtgtga                                                    >  7:273034/1‑146 (MQ=255)                                                                                     gCAGTTATTTCGCCGCACACAATCTGGCGAGCTTGGGGGCGGCAGTCAGCCCGGCGTGGTGTGGATTCAGGCGACTATCGCTCG‑CGGGCCCCCAGGGTTTGTGCTTCTAACTGATCGCCTGCGTGCTGGCGGGTAGCAGCCTTtgttc                                                    >  1:290436/1‑146 (MQ=255)                                                                                      cAGTTATTTCGCCGCACACAATCTGGCGAGCTTGGGGGCGGCAGTCAGCCCGGCGTGGTGTGGATTCA‑‑‑TACTATCGCTCG‑CGGGCCCCCAGGGTTTGTGCTTCTCa                                                                                          <  8:162715/106‑1 (MQ=255)                                                                                      cAGTTATTTCGCCGCACACAATCTGGCGAGCTTGGGGGCGGCAGTCAGCCCGGCGTGGTGTGGATTCA‑‑‑TACTATCGCTCG‑CGGGCCCCCAGGGTTTGTGCTTCTCa                                                                                          >  7:162715/1‑106 (MQ=255)                                                                                      cAGTTATTTCGCCGCACACAATCTGGCGAGCTTGGGGGCGGCAGTCAGCCCGGCGTGGTGTGGATTCA‑‑‑TACTATCGCTCG‑CGGGCCCCCAGGGTTTGTGCTTCTCACTGATCGCCTGCGTGCTGGCGGGTAGCAGCCTTTGTGCCATgc                                               <  6:133065/149‑1 (MQ=255)                                                                                       aGTTATTTCGCCGCACACAATCTGGCGAGCTTGGGGGCGGCAGTCAGCCCGGCGTGGTGTGGATTCA‑‑‑TACTATCGCTCG‑CGGGCCCCCAGGGTTTGTGCTTCTCACTGATCGCCTGCGTGCTGGCGGGTAGCAGCCTTTGTGCCATgcg                                              <  8:120509/149‑1 (MQ=255)                                                                                                gccgcACACAATCTGGCGAGCTTGGGGGCGGCAGTCAGCCCGGCGTGGTGTGGATTCA‑‑‑TACTATCGCTCG‑CGGGCCCCCAGGGTTTGTGCTTCTCACTGATCGCCTGCGTGCTGGCGGGTAGCAGCCTTTGTGCCATGCGCCCTCGACt                                     <  7:151656/149‑1 (MQ=255)                                                                                                 ccgcACACAATCTGGCGAGCTTGGGGGCGGCAGTCAGCCCGGCGTGGTGTGGATTCA‑‑‑TACTATCGCTCG‑CGGGCCCCCAGGGTTTGTGCTTCTCACTGATCGCCTGCGTGCTGGCGGGTAGCAGCCTTTTTGCCATGCGCCCTCGACt                                     >  5:179527/1‑148 (MQ=255)                                                                                                          aTCTGGCGAGCTTGGGGGCGGCAGTCAGCCCGGCGTGGTGTGGATTCA‑‑‑TACTATCGCTCG‑CGGGCCCCCAGGGTTTGTGCTTCTCACTGATCGCCTGCGTGCTGGCGGGTAGCAGCCTTTGTGCCATGCGCCCTCGACTGACCCCGGGc                           <  6:192019/149‑1 (MQ=255)                                                                                                            cTGGCGAGCTTGGGGGCGGCAGTCAGCCCGGCGTGGTGTGGATTCA‑‑‑TACTATCGCTCG‑CGGGCCCCCAGGGTTTGTGCTTCTCACTGATCGCCTGCGTGCTGGCGGGTAGCAGCCTTTGTGCCATGCGCCCTCGACTGACCCCGCGCa                          >  3:178192/1‑148 (MQ=255)                                                                                                                       gggggCGGCAGTCAGCCCGGCGTGGTGTGGATTCA‑‑‑TACTATCGCTCG‑CGGGCCCCCAGGGTTTGTGCTTCTCACTGATCGCCTGCGTGCTGGCGGGTAGCAGCCTTTGTGCCATGCGCCCTCGACTGACCCCGGGCAACTTTGCGCgg               <  3:177239/148‑1 (MQ=255)                                                                                                                         gggCGGCAGTCAGCCCGGCGTGGTGTGGATTCA‑‑‑TACTATCGCTCG‑CGGGCCCCCAGGGTTTGTGCTTCTCACTGATCGCCTGCGTGCTGGCGGGTAGCAGCCTTTGTGCCATGCGCCCTCGACTGACCCCGCGCAAAGTTGCCCggggt            <  4:178192/149‑2 (MQ=255)                                                                                                                           gcggcAGTCAGCCCGGCGTGGTGTGGATTCA‑‑‑TACTATCGCTCG‑CGGGCCCCCAGGGTTTGTGCTTCTCACTGATCGCCTGCGTGCTGGCGGGTAGCAGCCTTTGTGCCATGCGCCCTCGACTGACCCCGGGCAACTTTGCGCggg              >  6:204300/1‑145 (MQ=255)                                                                                                                                    aGCCCGGCGTGGTGTGGATTCA‑‑‑TACTATCGCTCG‑CGGGCCCCCAGGGTTTGTGCTTCTCACTGATCGCCTGCGTGCTGGCGGGTAGCAGCCTTTGTGCCATGCGCCCTCGACTGACCCCGGGCAACTTTGCGCGGGGAGATCTTTAAt  <  6:179527/148‑1 (MQ=255)                                                                                                                                       ccGGCGTGGTGTGGATTCA‑‑‑TACTATCGCTCG‑CGGGACCCCAGGGTTTGTGCTTCTCACTGATCGCATGCGTGCTGGCGCGTAGCAGCCATTGTGACAAGCGCACTCGACTGACACCGGGCAACttt                     >  7:104714/1‑126 (MQ=255)                                                                                                                                                   |                                                                                                                                         TGCTAGTTTTCACCCTTGGCGAGCTGCTGATTCAGCCAGCGGAGTATCTCTACATTGACTCGATCAGCCCGCCGCCCCTCAAAGGCAGTTATTTCGCCGCACACAATCTGGCGAGCTTGGGGGCGGCAGTCAGCCCGGCGTGGTGTGGATTCA‑‑‑TACTATCGCTCG‑CGGGCCCCCAGGGTTTGTGCTTCTCACTGATCGCCTGCGTGCTGGCGGGTAGCAGCCTTTGTGCCATGCGCCCTCGACTGACCCCGGGCAACTTTGCGCGGGGAGATCTTTAAT  >  NC_002947/4318683‑4318961

Alignment Legend
Aligned base mismatch/match (shaded by quality score): ATCG/ATCG < 3 ≤ ATCG/ATCG < 14 ≤ ATCG/ATCG < 21 ≤ ATCG/ATCG < 32 ≤ ATCG/ATCG < 36 ≤ ATCG/ATCG
Unaligned base: atcg    Masked matching base: atcg    Alignment gap: ‑    Deleted base: ‑