Predicted mutation
evidence	seq id	position	mutation	freq	annotation	gene	description
RA	NC_002947	2,907,700	T→A	14.9%	Q332L (CAG→CTG)	hasE ←	secretion metalloprotease

Read alignment evidence...
	seq id	position		ref	new	freq	score (cons/poly)	reads	annotation	genes	product
*	NC_002947	2,907,700	0	T	A	14.9%	108.4 / 11.1	47	Q332L (CAG→CTG)	hasE	secretion metalloprotease
Reads supporting (aligned to +/- strand):  ref base T (20/20);  new base A (2/5);  total (22/25)
Fisher's exact test for biased strand distribution p-value = 4.23e-01
Kolmogorov-Smirnov test that lower quality scores support variant p-value = 1.87e-01

CAGCCGGTCGGCGGAAATGGTTTTTACCCGGCCGGGAATGTTCGGCGTCTGCGCATGGTTGAAGGCCGGGAAGGCGATGTCCACGGCAAGGCCTGGGACCATCTTGTCGATCGCCTGCACCGGGATCATCGCATCGACCTGCAGCGGCTGGTCGAGCGGTACCACTTCCATGATCTTGGCCCCGGGCTGGATGATGCCGCCGACCGTGGCGATGCTCAGGCCCTGGACCATGCCGTCGATCGGCGAGCGGATCACCGTGTGGGTCACTTCATAGTCCAGTGCGCGCAAGCGGTC  >  NC_002947/2907552‑2907845                                                                                                                                                     |                                                                                                                                                  catccGGTCGGCGGAAATTGTTTTTACCCGGCCGGGAATGTTCGGCGTCTGCGCATGGTTGAAGGCCGGGAAGGCGATGTCCACGGCAAGGCCTGGGACCATCTTGTCGATCGCCTGCACCGGGATCATCGCATCGACCTGCAGCGGCt                                                                                                                                                   <  4:225363/146‑1 (MQ=255)    ccGGTCGGCGGAAATGGTTTTTACCCGGCCGGGAATGTTCGGCGTCTGCGCATGGTTGAAGGCCGGGAAGGCGATGTCCACGGCAAGGCCTGGGACCATCTTGTCGATCGCCTGCACCGGGATCATCGCATCGACCTGCAGCGGCTGGt                                                                                                                                                >  1:289131/1‑149 (MQ=255)    ccGGTCGGCGGAAATGGTTTTTACCCGGCCGGGAATGTTCGGCGTCTGCGCATGGTTGAAGGCCGGGAAGGCGATGTCCACGGCAAGGCCTGGGACCATCTTGTCGATCGCCTGCACCGGGATCATCGCATCGACCTGCAGCGGCTGGt                                                                                                                                                >  6:339583/1‑149 (MQ=255)     cGGTCGGCGGAAATGGTTTTTACCCGGCCGGGAATGTTCGGCGTCTGCGCATGGTTGAAGGCCGGGAAGGCGATGTCCACGGCAAGGCCTGGGACCATCTTGTCGATCGCCTGCACCGGGATCATCGCATCGACCTGCAGCGGCTGGTc                                                                                                                                               <  1:328532/149‑1 (MQ=255)      ggTCGGCGGAAATGGTTTTTACCCGGCCGGGAATGTTCGGCGTCTGCGCATGGTTGAAGGCCGGGAAGGCGATGTCCACGGCAAGGCCTGGGACCATCTTGTCGATCGCCTGCACCGGGATCATCGCATCGACCAGCCGCTGCAGGTCg                                                                                                                                              <  1:198486/149‑1 (MQ=255)        tCGGCGGAAATGGTTTTTACCCGGCCGGGAATGTTCGGCGTCTGCGCATGGTTGAAGGCCGGGAAGGTGATGTCCACGGCAAGGCCTGGGACCATCTTGTCGATCGCCTGCACCGGGATCATCGCATCGACCAGCCGCTGCAGGTCGat                                                                                                                                            <  6:21461/149‑2 (MQ=255)        tCGGCGGAAATGGTTTTTACCCGGCCGGGAATGTTCGGCGTCTGCGCATGGTTGAAGGCCGGGAAGGCGATGTCCACGGCAAGGCCTGGGACCATCTTGTCGATCGCCTGCACCGGGATCATCGCATCGACCAGCCGCTGCAGGTCGat                                                                                                                                            <  3:68251/149‑2 (MQ=255)          ggcggAAATGGTTTTTACCCGGCCGGGAATGTTCGGCGTCTGCGCATGGTTGAAGGCCGGGAAGGCGATGTCCACGGCAAGGCCTGGGACCATCTTGTCGATCGCCTGCACCGGGATCATCGCATCGACCTGCAGCGGCTGGTCGAGc                                                                                                                                           <  3:60655/148‑1 (MQ=255)          ggcggAAATGGTTTTTACCCGGCCGGGAATGTTCGGCGTCTGCGCATGGTTGAAGGCCGGGAAGGCGATGTCCACGGCAAGGCCTGGGACCATCTTGTCGATCGCCTGCACCGGGATCATCGCATCGACCAGCCGCTGCAGGTCGatg                                                                                                                                           <  1:47216/148‑3 (MQ=255)              gAAATGGTTTTTACCCGGCCGGGAATGTTCGGCGTCTGCGCATGGTTGAAGGCCGGGAAGGCGATGTCCACGGCAAGGCCTGGGACCATCTTGTCGATCGCCTGCACCGGGATCATCGCATCGACCTGCAGCGGCTGGTCGAGCGGTAc                                                                                                                                      <  3:301657/149‑1 (MQ=255)               aaaTGGTTTTTACCCGGCCGGGAATGTTCGGCGTCTGCGCATGGTTGAAGGCCGGGAAGGCGATGTCCACGGCAAGGCCTGGGACCATCTTGTCGATCGCCTGCACCGGGATCATCGCATCGACCTGCAGCGGCTGGTCGAGCGGTAcc                                                                                                                                     <  3:285128/149‑1 (MQ=255)                      ttttACCCGGCCGGGAATGTTCGGCGTCTGCGCATGGTTGAAGGCCGGGAAGGCGATGTCCACGGCAAGGCCTGGGACCATCTTGTCGATCGCCTGCGCCGGGATCATCGCATCGCCCTGCAGCGGCTGGTCGAGCGGTACCACTTcc                                                                                                                               >  8:174010/1‑148 (MQ=255)                           cccGGCCGGGAATGTTCGGCGTCTGCGCATGGTTGAAGGCCGGGAAGGCGATGTCCACGGCAAGGCCTGGGACCATCTTGTCGATCGCCTGCACCGGGATCATCGCATCGACCTGCAGCGGCTGGTCGAGCGGTACCACTTCCATGAt                                                                                                                          <  1:305741/148‑1 (MQ=255)                                  gggAATGTTCGGCGTCTGCGCATGGTTGAAGGCCGGGAAGGCGATGTCCACGGCAAGGCCTGGGACCATCTTGTCGATCGCCTGCACCGGGATCATCGCATCGACCTGCAGCGGCTGGTCGAGCGGTACCACTTCCATGATCTTGGccc                                                                                                                  <  5:339583/149‑1 (MQ=255)                                   ggAATGTTCGGCGTCTGCGCATGGTTGAAGGCCGGGAAGGCGATGTCCACGGCAAGGCCTGGGACCATCTTGTCGATCGCCTGCACCGGGATCATCGTATCGACCTGCAGCGGCTGGTCGAGCGGTACCACTTCCATGATCTTGGcccc                                                                                                                 <  5:3504/149‑1 (MQ=255)                                    gAATGTTCGGCGTCTGCGCATGGTTGAAGGCCGGGAAGGCGATGTCCACGGCAAGGCCTGGGACCATCTTGTCGATCGCCTGCACCGGGATCATCGCATCGACCTGCAGCGGCTGGTCGAGCGGTACCACTTCCATGATCTTGGCCCCg                                                                                                                >  5:237894/1‑149 (MQ=255)                                         ttCGGCGTCTGCGCATGGTTGAAGGCCGGGAAGGCGATGTCCACGTCAAGGCCTGGGACCATCTTGTCGATCGCCTGCACCGGGATCATCGCATCGACCTGCAGCGGCTGGTCGAGCGGTACCACTTCCATGATCTTGGCCCCGGGcag                                                                                                           <  8:384387/149‑3 (MQ=255)                                                       aTGGTTGAAGGCCGGGAAGGCGATGTCCACGGCAAGGCCTGGGACCATCTTGTCGATCGCCTGCACCGGGATCATCGCATCGACCTGCAGCGGCTGGTCGAGCGGTACCACTTCCATGATCTTGGCCCCGGGCTGGATGATGCCGCCGa                                                                                             >  1:32802/1‑149 (MQ=255)                                                                     ggAAGGCGATGTCCACGGCAAGGCCTGGGACCATCTTGTCGATCGCCTGCACCGGGATCATCGCATCGACCTGCAGCGGCTGGTCGAGCGGTACCACTTCCATGATCTTGGCCCCGGGCTGGATGATGCCGCCGACCGTGGCGATGCTc                                                                               <  4:368681/149‑1 (MQ=255)                                                                      gAAGGCGATGTCCACGGCAAGGCCTGGGACCATCTTGTCGATCGCCTGCACCGGGATCATCGCATCGACCTGCAGCGGCTGGTCGAGCGGTACCACTTCCATGATCTTGGCCCCGGGCTGGATGATGCCGCCGACCGTGGCGATGCt                                                                                >  7:91402/1‑147 (MQ=255)                                                                        aGGCGATGTCCACGGCAAGGCCTGGGACCATCTTGTCGATCGCCTGCACCGGGATCATCGCATCGACCTGCAGCGGCTGGTCGAGCGGTACCACTTCCATGATCTTGGCCCCGGGCTGGATGATGCCGCCGACCGTGGCGATGCTCAgg                                                                            <  2:289131/149‑1 (MQ=255)                                                                         ggCGATGTCCACGGCAAGGCCTGGGACCATCTTGTCGATCGCCTGCACCGGGATCATCGCATCGACCTGCAGCGGCTGGTCGAGCGGTACCACTTCCATGATCTTGGCCCCGGGCTGGATGATGCCGCCGACCGTGGCGATGCTCAGGc                                                                           >  2:363821/1‑149 (MQ=255)                                                                             aTGTCCACGGCAAGGCCTGGGACCATCTTGTCGATCGCCTGCACCGGGATCATCGCATCGACCTGCAGCGGCTGGTCGAGCGGTACCACTTCCATGATCTTGGCCCCGGGCTGGATGATGCCGCCGACCGTGGCGATGCTCAGGCCCTg                                                                       <  7:348339/149‑1 (MQ=255)                                                                                tCCACGGCAAGGCCTGGGACCATCTTGTCGATCGCCTGCACCGGGATCATCGCATCGACCTGCAGCGGCTGGTCGAGCGGTACCACTTCCATGATCTTGGCCCCGGGCTGGATGATGCCGCCGACCGTGGCGATGCTCAGGCCCTGGAc                                                                    >  8:49718/1‑149 (MQ=255)                                                                                 ccACGGCAAGGCCTGGGACCATCTTGTCGATCGCCTGCACCGGGATCATCGCATCGACCTGCAGCGGCTGGTCGAGCGGTACCACTTCCATGATCTTGGCCCCGGGCTGGATGATGCCGCCGACCGTGGCGATGCTCAGGccc                                                                         >  1:132390/1‑143 (MQ=255)                                                                                 ccACGGCAAGGCCTGGGACCATCTTGTCGATCGCCTGCACCGGGATCATCGCATCGACCTGCAGCGGCTGGTCGAGCGGTACCACTTCCATGATCTTGGCCCCGGGCTGGATGATGCCGCCGACCGTGGCGATGCTCAGGccc                                                                         <  2:132390/143‑1 (MQ=255)                                                                                 ccACGGCAAGGCCTGGGACCATCTTGTCGATCGCCTGCACCGGGATCATCGCATCGACCTGCAGCGGCTGGTCGAGCGGTACCACTTCCATGATCTTGGCCCCGGGCTGGATGATGCCGCCGACCGTGGCGATGCTCAGGCCCTGGAc                                                                    >  4:299879/1‑148 (MQ=255)                                                                                 ccACGGCAAGGCCTGGGACCATCTTGTCGATCGCCTGCACCGGGATCATCGCATCGACCTGCAGCGGCTGGTCGAGCGGTACCACTTCCATGATCTTGGCCCCGGGCTGGATGATGCCGCCGACCGTGGCGATGCTCAGGCCCTGGAc                                                                    >  7:252270/1‑148 (MQ=255)                                                                                  cACGGCAAGGCCTGGGACCATCTTGTCGATCGCCTGCACCGGGATCATCGCATCGACCTGCAGCGGCTGGTCGAGCGGTACCACTTCCATGATCTTGGCCCCGGGCTGGATGATGCCGCCGACCGTGGCGATGCTCAGGCCCTGGACCa                                                                  >  7:30685/1‑149 (MQ=255)                                                                                             cTGGGACCATCTTGTCGATCGCCTGCACCGGGATCATCGCATCGACCTGCAGCGGCTGGTCGAGCGGTACCACTTCCATGATCTTGGCCCCGGGCTGGATGATGCCGCCGACCGTGGCGATGCTCAGGCCCTGGACCATGCCGTCGATc                                                       >  3:316161/1‑149 (MQ=255)                                                                                                ggACCATCTTGTCGATCGCCTGCACCGGGATCATCGCATCGACCTGCAGCGGCTGGTCGAGCGGTACCACTTCCATGATCTTGGCCCCGGGCTGGATGATGCCGCCGACCGTGGCGATGCTCAGGCCCTGGACCATGCCGTCGATCGGc                                                    <  8:91402/149‑1 (MQ=255)                                                                                                        ttGTCGATCGCCTGCACCGGGATCATCGCATCGACCTGCAGCGGCTGGTCGAGCGGTACCACTTCCATGATCTTGGCCCCGGGCTGGATGATGCCGCCGACCGTGGCGATGCTCAGGCCCTGGACCATGCCGTCGATCGGCGAGCGGAt                                            >  4:134207/1‑149 (MQ=255)                                                                                                              aTCGCCTGCACCGGGATCATCGCATCGACCTGCAGCGGCTGGTCGAGCGGTACCACTTCCATGATCTTGGCCCCGGGCTGGATGATGCCGCCGACCGTGGCGATGCTCAGGCCCTGGACCATGCCGTCGATCGGCGAGCGGATCACCgt                                      <  3:299879/149‑1 (MQ=255)                                                                                                                 gCCTGCACCGGGATCATCGCATCGACCTGCAGCGGCTGGTCGCGCGGTACCAATTACAAGAGCTTGGCCCCGGGGTGGATGATTCCGCCGACCGTGGCGATGCTCAGGCCCTGGACCATGCCGTCGATCGGCGAGCTGATCACCGagtg                                   >  6:123784/1‑149 (MQ=255)                                                                                                                 gCCTGCACCGGGATCATCGCATCGACCTGCAGCGGCTGGTCGAGCGGTACCACTTCCATGATCTTGGCCCCGGGCTGGATGATGCCGCCGACCGTGGCGATGCTCAGGCCCTGGACCATGCCGTCGATCGGCGAGCGGATCACCgtgt                                    <  3:134207/148‑1 (MQ=255)                                                                                                                                atcgcatcgACCTGCAGCGGCTGGTCGAGCGGTACCACTTCCATGATCTTGGCCCCGGGCTGGATGATGCCGCCGACCGTGGCGATGCTCAGGCCCTGGACCATGCCGTCGATCGGCGAGCGGATCACCGTGTGGGTCACTTCATAGTc                    >  2:298542/1‑149 (MQ=255)                                                                                                                                atcgcatcgACCTGCAGCGGCTGGTCGAGCGGTACCACTTCCATGATCTTGGCCCCGGGCTGGATGATGCCGCCGACCGTGGCGATGCTCAGGCCCTGGACCATGCCGTCGATCGGCGAGCGGATCACCGTGTGGGTCACTTCATAGTc                    >  1:79718/1‑149 (MQ=255)                                                                                                                                      tcgACCAGCCGCTGCAGGTCGAGCGGTACCATTTCCATGATCTTGGCCCCGGGCTGGATGATGCCGCCGACCGTGGCGATGCTCAGGCCCTgg                                                                      <  1:124875/93‑1 (MQ=255)                                                                                                                                      tcgACCAGCCGCTGCAGGTCGAGCGGTACCACTTCCATGATCTTGGCCCCGGGCTGGATGATGCCGCCGACCGTGGCGATGCTCAGGCCCTgg                                                                      >  2:124875/1‑93 (MQ=255)                                                                                                                                      tcgACCAGCCGCTGCAGGTCGAGCGGTACCACTTCCATGATCTTGGCCCCGGGCTGGATGATGCCGCCGACCGTGGCGATGCTCAGGCCCTGGACCATGCCGTCGATCGGCGAGCGGATGACCGTGTGGGTCACTTCATAGTCCAGTgc              >  5:387221/1‑149 (MQ=255)                                                                                                                                        gACCTGCAGCGGCTGGTCGAGCGGTACCACTTCCATGATCTTGGCCCCGGGCTGGATGATGCCGCCGACCGTGGCGATGCTCAGGCCCTGGACCATGCCGTCGATCGGCGAGCGGATCACCGTGTGGGTCACTTCATAGTCCAGTgcgc            <  2:79718/149‑1 (MQ=255)                                                                                                                                         aCCTGCAGCGGCTGGTCGAGCGGTACCACTTCCATGATCTTGGCCCCGGGCTGGATGATGCCGCCGACCGTGGCGATGCTCAGGCCCTGGACCATGCCGTCGATCGGCGAGCGGATCACCGTGTGGGTCACTTCATAGTCCAGTgcgcg           >  3:363406/1‑149 (MQ=255)                                                                                                                                         aCCTGCAGCGGCTGGTCGAGCGGTACCACTTCCATGATCTTGGCCCCGGGCTGGATGATGCCGCCGACCGTGGCGATGCTCAGGCCCTGGACCATGCCGTCGATCGGCGAGCGGATCACCGTGTGGGTCACTTCATAGTCCAGTgcgcg           <  7:49718/149‑1 (MQ=255)                                                                                                                                             gCAGCGGCTGGTCGAGCGGTACCACTTCCATGATCTTGGCCCCGGGCTGGATGATGCCGCCGACCGTGGCGATGCTCAGGCCCTGGACCATGCCGTCGATCGGCGAGCGGATCACCGTGTGGGTCACTTCATAGTCCAGTGCGCGCAAg       >  7:248467/1‑149 (MQ=255)                                                                                                                                              cAGCGGCTGGTCGAGCGGTACCACTTCCATGATCTTGGCCCCGGGCTGGATGATGCCGCCGACCGTGGCGATGCTCAGGCCCTGGACCATGCCGTCGATCGGCGAGCGGATCACCGTGTGGGTCACTTCATAGTCCAGTGCGCGCaa        <  2:32802/147‑1 (MQ=255)                                                                                                                                              cAGCGGCTGGTCGAGCGGTACCACTTCCATGATCTTGGCCCCGGGCTGGATGATGCCGCCGACCGTGGCGATGCTCAGGCCCTGGACCATGCCGTCGATCGGCGAGCGGATCACCGTGTGGGTCACTTCATAGTCCAGTGCGCGCAAg       <  4:316161/148‑1 (MQ=255)                                                                                                                                              cAGCGGCTGGTCGAGCGGTACCACTTCCATGATCTTGGCCCCGGGCTGGATGATGCCGCCGACCGTGGCGATGCTCAGGCCCTGGACCATGCCGTCGATCGGCGAGCGGATCACCGTGTGGGTCACTTCATAGTCCAGTGCGCGCAAGc      >  3:320784/1‑149 (MQ=255)                                                                                                                                                  ggCTGGTCGAGCGGTACCACTTCCATGATCTTGGCCCCGGGCTGGATGATGCCGCCGACCGTGGCGATGCTCAGGCCCTGGACCATGCCGTCGATCGGCGAGCGGATCACCGTGTGGGTCACTTCATAGTCCAGTGCGCGCAAGCGGTc  <  6:237894/149‑1 (MQ=255)                                                                                                                                                     |                                                                                                                                                  CAGCCGGTCGGCGGAAATGGTTTTTACCCGGCCGGGAATGTTCGGCGTCTGCGCATGGTTGAAGGCCGGGAAGGCGATGTCCACGGCAAGGCCTGGGACCATCTTGTCGATCGCCTGCACCGGGATCATCGCATCGACCTGCAGCGGCTGGTCGAGCGGTACCACTTCCATGATCTTGGCCCCGGGCTGGATGATGCCGCCGACCGTGGCGATGCTCAGGCCCTGGACCATGCCGTCGATCGGCGAGCGGATCACCGTGTGGGTCACTTCATAGTCCAGTGCGCGCAAGCGGTC  >  NC_002947/2907552‑2907845

Alignment Legend
Aligned base mismatch/match (shaded by quality score): ATCG/ATCG < 3 ≤ ATCG/ATCG < 14 ≤ ATCG/ATCG < 27 ≤ ATCG/ATCG < 32 ≤ ATCG/ATCG < 36 ≤ ATCG/ATCG
Unaligned base: atcg    Masked matching base: atcg    Alignment gap: ‑    Deleted base: ‑