Predicted mutation
evidence	seq id	position	mutation	freq	annotation	gene	description
RA	NC_002947	2,907,691	T→A	15.6%	Q335L (CAG→CTG)	hasE ←	secretion metalloprotease

Read alignment evidence...
	seq id	position		ref	new	freq	score (cons/poly)	reads	annotation	genes	product
*	NC_002947	2,907,691	0	T	A	15.6%	104.6 / 11.3	45	Q335L (CAG→CTG)	hasE	secretion metalloprotease
Reads supporting (aligned to +/- strand):  ref base T (18/20);  new base A (2/5);  total (20/25)
Fisher's exact test for biased strand distribution p-value = 4.37e-01
Kolmogorov-Smirnov test that lower quality scores support variant p-value = 3.71e-01

TCGAGCAGCCGGTCGGCGGAAATGGTTTTTACCCGGCCGGGAATGTTCGGCGTCTGCGCATGGTTGAAGGCCGGGAAGGCGATGTCCACGGCAAGGCCTGGGACCATCTTGTCGATCGCCTGCACCGGGATCATCGCATCGACCTGCAGCGGCTGGTCGAGCGGTACCACTTCCATGATCTTGGCCCCGGGCTGGATGATGCCGCCGACCGTGGCGATGCTCAGGCCCTGGACCATGCCGTCGATCGGCGAGCGGATCACCGTGTGGGTCACTTCATAGTCCAGTGCGCG  >  NC_002947/2907547‑2907836                                                                                                                                                 |                                                                                                                                                  tcgAGCAGCCGGTCGGCGGAAATGGTTTTTACCCGGCCGGGAATGTTCGGCGTCTGCGCATGGTTGAAGGCCGGGAAGGCGATGTCCACGGCAAGGCCTGGGACCATCTTGTCGATCGCCTGCACCGGGATCATCGCATCGACCTGCAg                                                                                                                                               <  3:429916/149‑1 (MQ=255)     gcagcCGGTCGGCGGAAATGGTTTTTACCCGGCCGGGAATGTTCGGCGTCTGCGCATGGTTGAAGGCCGGGAAGGCGATGTCCACGGCAAGGCCTGGGACCATCTTGTCGATCGCCTGCACCGGGATCATCGCATCGACCTGCAGCGGc                                                                                                                                           <  6:391034/149‑1 (MQ=255)      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  <  7:49718/149‑1 (MQ=255)                                                                                                                                              aCCTGCAGCGGCTGGTCGAGCGGTACCACTTCCATGATCTTGGCCCCGGGCTGGATGATGCCGCCGACCGTGGCGATGCTCAGGCCCTGGACCATGCCGTCGATCGGCGAGCGGATCACCGTGTGGGTCACTTCATAGTCCAGTgcgcg  >  3:363406/1‑149 (MQ=255)                                                                                                                                                 |                                                                                                                                                  TCGAGCAGCCGGTCGGCGGAAATGGTTTTTACCCGGCCGGGAATGTTCGGCGTCTGCGCATGGTTGAAGGCCGGGAAGGCGATGTCCACGGCAAGGCCTGGGACCATCTTGTCGATCGCCTGCACCGGGATCATCGCATCGACCTGCAGCGGCTGGTCGAGCGGTACCACTTCCATGATCTTGGCCCCGGGCTGGATGATGCCGCCGACCGTGGCGATGCTCAGGCCCTGGACCATGCCGTCGATCGGCGAGCGGATCACCGTGTGGGTCACTTCATAGTCCAGTGCGCG  >  NC_002947/2907547‑2907836

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: ‑