Predicted mutation
evidence	seq id	position	mutation	freq	annotation	gene	description
RA	NC_002947	4,424,884	T→C	8.9%	H20R (CAT→CGT)	PP_5647 ←	hypothetical protein

Read alignment evidence...
	seq id	position		ref	new	freq	score (cons/poly)	reads	annotation	genes	product
*	NC_002947	4,424,884	0	T	C	8.9%	124.5 / 2.9	45	H20R (CAT→CGT)	PP_5647	hypothetical protein
Reads supporting (aligned to +/- strand):  ref base T (19/22);  new base C (2/2);  total (21/24)
Fisher's exact test for biased strand distribution p-value = 1.00e+00
Kolmogorov-Smirnov test that lower quality scores support variant p-value = 9.62e-01

GCTTGGTCTGGTGCTGTAAGCCTCTTCTACAATTCGGTCCCCGCTTTTGGAGTACACCCCGATGAAGAGCTGCGTTTCGCCTGTCCGCGAAAGACGGGTTTGCACGTCGATACTCCTGCCGTCCTCAAGGATTTCGTCGTGATGACGAAGGTGAAGCGC‑TGGGTCTGCCCAGGTCCAGAATTTTTCGCCGCGACATCTCATATCAATCTCCTCTTACTTATCCCAGTAGGCGCGGTAAAGAGAGGGATAGATATCCATTTCGCTTAAATGCGACCGGTG  >  NC_002947/4424742‑4425020                                                                                                                                               |                                                                                                                                          gCTTGGTCTGGTGATGTAAGCCACATCTACAATTCGGTCCCCGCTTTTGGAGTACACCCCGATGAAGAGCTGCGTTTCGCCTGTCCGCGAAAGACGGGTTTGCACGTCGATACTCCTGCCGTCCTCAAGGATTTCGTCGTCATGACg                                                                                                                                       >  8:162817/1‑147 (MQ=255)  cTTGGTCTGGTGCTGTAAGCCTCTTCTACAATTCGGTCCCCGCTTTTGGAGTACACCCCGATGAAGAGCTGCGTTTCGCCTGTCCGCGAAAGACGGGTTTGCACGTCGATACTCCTGCCGTCCTCAAGGATTTCGTCGTGATGACGAAg                                                                                                                                    <  6:82830/149‑1 (MQ=255)      gTCTGGTGCTGTAAGCCTCTTCTACAATTCGGTCCCCGCTTTTGGAGTACACCCCGATGAAGAGCTGCGTTTCGCCTGTCCGCGAAAGACGGGTTTGCACGTCTATACTCCTGCCGTCCTCAAGGATTTCGTCATCACGACGaaatcc                                                                                                                                 <  5:47261/148‑5 (MQ=255)       tCTGGTGCTGTAAGCCTCTTCTACAATTCGGTCCCCGCTTTTGGAGTACACCCCGATGAAGAGCTGCGTTTCGCCTGTCCGCGAAAGACGGGTTTGCACGTCGATACTCCTGCCGTCCTCAAGGATTTCGTCGTGATGACGAAGGTGaa                                                                                                                               <  4:190963/149‑1 (MQ=255)       tCTGGTGCTGTAAGCCTCTTCTACAATTCGGTCCCCGCTTTTGGAGTACACCCCGATGAAGAGCTGCGTTTCGCCTGTCCGCGAAAGACGGGTTTGCACGTCGATACTCCTGCCGTCCTCAAGGATTTCGTCATCACGACGaaatcc                                                                                                                                 >  6:314480/1‑143 (MQ=255)       tCTGGTGCTGTAAGCCTCTTCTACAATTCGGTCCCCGCTTTTGGAGTACACCCCGATGAAGAGCTGCGTTTCGCCTGTCCGCGAAAGACGGGTTTGCACGTCGATACTCCTGCCGTCCTCAAGGATTTCGTCATCACGACGaaatcc                                                                                                                                 <  5:314480/147‑5 (MQ=255)           gTGCTGTAAGCCTCTTCTACAATTCGGTCCCCGCTTTTGGAGTACACCCCGATGAAGAGCTGCGTTTCGCCTGTCCGCGAAAGACGGGTTTGCACGTCGATACTCCTGCCGTCCTCAAGGATTTCGTCGTGATGACGAAGGTGAAgcgc                                                                                                                           >  2:132392/1‑149 (MQ=255)                gTAAGCCTCTTCTACAATTCGGTCCCCGCTTTTGGAGTACACCCCGATGAAGAGCTGCGTTTCGCCTGTCCGCGAAAGACGGGTTTGCACGTCGATACTCCTGCCGTCCTCAAGGATTTCGTCGTGATGACGAAGGTGAAGCGC‑Tggg                                                                                                                      >  4:290503/1‑148 (MQ=255)                 tAAGCCTCTTCTACAATTCGGTCCCCGCTTTTGGAGTACACCCCGATGAAGAGCTGCGTTTCGCCTGTCCGCGAAAGACGGGTTTGCACGTCGATACTCCTGCCGTCCTCAAGGATTTCGTCGTGATGACGAAGGTGAAGCGC‑TGGGt                                                                                                                     <  2:11731/148‑1 (MQ=255)                     ccTCTTCTACAATTCGGTCCCCGCTTTTGGAGTACACCCCGATGAAGAGCTGCGTTTCGCCTGTCCGCGAAAGACGGGTTTGCACGTCGATACTCCTGCCGTCCTCAAGGATTTCGTCGTGATGACGAAGGTGAAGCGC‑TGGGTCTGcc                                                                                                                <  1:132392/149‑1 (MQ=255)                     ccTCTTCTACAATTCGGTCCCCGCTTTTGGAGTACACCCCGATGAAGAGCTGCGTTTCGCCTGTCCGCGAAAGACGGGTTTGCACGTCGATACTCCTGCCGTCCTCAAGGATTTCGTCGTGATGACGAAGGTGAAGCGC‑TGGGTCTGcc                                                                                                                <  7:188785/149‑1 (MQ=255)                      ctctTCTACAATTCGGTCCCCGCTTTTGGAGTACACCCCGATGAAGAGCTGCGTTTCGCCTGTCCGCGAAAGACGGGTTTGCACGTCGATACTCCTGCCGTCCTCAAGGATTTCGTCGTGATGACGAAGGTGAAGCGC‑TGGGTCTg                                                                                                                  <  5:170220/146‑1 (MQ=255)                      ctctTCTACAATTCGGTCCCCGCTTTTGGAGTACACCCCGATGAAGAGCTGCGTTTCGCCTGTCCGCGAAAGACGGGTTTGCACGTCGATACTCCTGCCGTCCTCAAGGATTTCGTCGTGATGACGAAGGTGAAGCGC‑TGGGTCTg                                                                                                                  >  6:170220/1‑146 (MQ=255)                       tcctctACAATTCGGTCCCCGCTTTTGGAGTACACCCCGATGAAGAGCTGCGTTTCGCCTGTCCGCGAAAGACGGGTTTGCACGTCGATACTCCTGCCGTCCTCAAGGATTTCGTCGTGATGACGAAGGTGAAGCGC‑TGGGTCTGcc                                                                                                                >  2:230029/4‑147 (MQ=255)                          tctACAATTCGGTCCCCGCTTTTGGAGTACACCCCGATGAAGAGCTGCGTTTCGCCTGTCCGCGAAAGACGGGTTTGCACGTCGATACTACTGACGTCCTCAAGGATTTCGTCGTGATGACGAAGGTGAAGCGC‑TGGGTCTGCCCAGGt                                                                                                           >  5:303030/1‑149 (MQ=255)                                     gTCCCCGCTTTTGGAGTACACCCCGATGAAGAGCTGCGTTTCTCCTGTCCGCGAAAGACGGGTTTGCACGTCGATACTCCTGCCGTCCTCAAGGATTTCGTCGTGATGACGAAGGTGAAGCGC‑TGGGTCTGCCCAGGTCCAGAAttttt                                                                                                <  6:251209/149‑1 (MQ=255)                                     gTCCCCGCTTTTGGAGTACACCCCGATGAAGAGCTGCGTTTCGCCTGTCCGCGAAAGACGGGTTTGCACGTCGATACTCCTGCCGTCCTCAAGGATTTCGTCGTGATGACGAAGGTGAAgc                                                                                                                             >  2:152041/1‑121 (MQ=255)                                     gTCCCCGCTTTTGGAGTACACCCCGATGAAGAGCTGCGTTTCGCCTGTCCGCGAAAGACGGGTTTGCACGTCGATACTCCTGCCGTCCTCAAGGATTTCGTCGTGATGACGAAGGTGAAgc                                                                                                                             <  1:152041/121‑1 (MQ=255)                                      tCCCCGCTTTTGGAGTACACCCAGATGAAGAGCTGCGTTTCGCCTGTCCGCGAAAGACGGGTTTGAACGTCGATACTCCTGCCGTCCTCAAGGATTTCGTCGTGATGACGAAGGTGAAGCGC‑TGGGTCTGCCCAGGTCCAGAATTTTTc                                                                                               <  8:132956/149‑1 (MQ=255)                                                          cccGATGAAGAGCTGCGTTTCGCCTGTCCGCGAAAGACGGGTTTGCACGTCGATACTCCTGCCGTCCTCAAGGATTTCGTCGTGATGAc                                                                                                                                        >  5:307070/1‑89 (MQ=255)                                                          cccGATGAAGAGCTGCGTTTCGCCTGTCCGCGAAAGACGGGTTTGCACGTCGATACTCCTGCCGTCCTCAAGGATTTCGTCGTGATGAc                                                                                                                                        <  6:307070/89‑1 (MQ=255)                                                          cccGATGAAGAGCTGCGTTTCGCCTGTCCGCGAAAGACGGGTTTGCACGTCGATACTCCTGCCGTCCTCAAGGATTTCGTCGTGATGACGAAGGTGAAGCGC‑TGGGTCTGCCCAGGTCCAGAATTTTTCGCCGCGACATCTCATATCaa                                                                           >  3:89831/1‑149 (MQ=255)                                                            cGATGAAGAGCTGCGTTTCGCCTGTCCGCGAAAGACGGGTTTGCACGTCGATACTCCTGCCGTCCTCAAGGATATCGTCGTGATGACGAAGGTGAAGCGCTTGGGTCTGCCCAGGTCCAGAATTTTTCGCCGCGACATCTCATATCAAt                                                                          <  1:232786/149‑1 (MQ=255)                                                             gATGAAGAGCTGCGTTTCGCCTGTCCGCGAAAGACGGGTTTGCACGTCGATACTCCTGCCGTCCTCAAGGATTTCGTCGTGATGACGAAGGTGAAGCGC‑TGGGTCTGCCCAg                                                                                                             >  1:116394/1‑112 (MQ=255)                                                             gATGAAGAGCTGCGTTTCGCCTGTCCGCGAAAGACGGGTTTGCACGTCGATACTCCTGCCGTCCTCAAGGATTTCGTCGTGATGACGAAGGTGAAGCGC‑TGGGTCTGCCCAg                                                                                                             <  2:116394/112‑1 (MQ=255)                                                              aTGAAGAGCTGCGTTTCGCCTGTCCGCGAAAGACGGGTTTGCACGTCGATACTCCTGCCGTCCTCAAGGATTTCGTCGTGATGACGAAGGTGAAGCGC‑TGGGTCTGCCCAGGTCCAGAATTTTTCGCCGCGACATCTCATATCAAtctc                                                                       <  6:287711/149‑1 (MQ=255)                                                                        gCGTTTCGCCTGTCCGCGAAAGACGGGTTTGCACGTCGATACTCCTGCCGTCCTCAAGGATTTCGTCGTGATGACGAAGGTGAAGCGC‑TGGGTCTGCCCAGGTCCAGAATTTTTCGCCGCGACATCTCATATCAATCTCCTcttactta                                                             >  6:102024/1‑149 (MQ=255)                                                                         cGTTTCGCCTGTCCGCGAAAGACGGGTTTGCACGTCGATACTCCTGCCGTCCTCAAGGATTTCGTCGTGATGACGAAGGTGAAGCGC‑TGGGTCTGCCCAGGTCCAGAATTTTTCGCCGCGACATCTCATATCAATCTCCTCTTACTTAt                                                            <  3:156857/149‑1 (MQ=255)                                                                            ttCGCCTGTCCGCGAAAGACGGGTTTGCACGTCGATACTCCTGCCGTCCTCAAGGATTTCGTCGTGATGACGAAGGTGAAGCGC‑TGGGTCTGCCCAGGTCCAGAAttttt                                                                                                >  4:77949/1‑110 (MQ=255)                                                                            ttCGCCTGTCCGCGAAAGACGGGTTTGCACGTCGATACTCCTGCCGTCCTCAAGGATTTCGTCGTGATGACGAAGGTGAAGCGC‑TGGGTCTGCCCAGGTCCAGAAttttt                                                                                                <  3:77949/110‑1 (MQ=255)                                                                                ccTGTCCGCGAAAGACGGGTTTGCACGTCGATACTCCTGCCGTCCTCAAGGATTTCGTCGTGATGACGAAGGTGAAGCGC‑TGGGTCTGCCCAGGTCCAGAATTTTTCGCCGCGACATCTCATATCAATCTCCTCTTACTTATCCCAg                                                       >  4:288403/1‑147 (MQ=255)                                                                                 cTGTCCGCGAAAGACGGGTTTGCACGTCGATACTCCTGCCGTCCTCAAGGATTTCGTCGTGATGACGAAGGTGAGGCGC‑TGGGTCTGCCCAGGTCCAGAATTTTTCGCCGCGACATCTCATATCAATCTCCTCTTACTTATCCCAGTAg                                                    <  7:226094/149‑1 (MQ=255)                                                                                    tCCGCGAAAGACGGGTTTGCACGTCGATACTCCTGCCGTCCTCAAGGATTTCGTCGTGATGACGAAGGTGAAGCGC‑TGGGTCTGCCCAGGTCCAGAATTTTTCGCCGCGACATCTCATATCAATCTCCTCTTACTTATCCCAGTAGgcg                                                 >  5:18677/1‑149 (MQ=255)                                                                                      cgcgAAAGACGGGTTTGCACGTCGATACTCCTGCCGTCCTCAAGGATTTCGTCGTGATGACGAAGGTGAAGCGC‑TGGGTCTGCCCAGGTCCAGAATTTTTCGCCGCGACATCTCATATCAATCTCCTCTTACTTATCCCAGTAGGcgcg                                               >  2:53973/1‑149 (MQ=255)                                                                                          aaaGACGGGTTTGCACGTCGATACTCCTGCCGTCCTCAAGGATTTCGTCGTGATGACGAAGGTGAAGCGC‑TGGGTCTGCCCAGGTCCAGAATTTTTCGCCGCGACATCTCATATCAATCTCCTCTTACTTATCCCAGTAGGCGCGGTa                                            >  8:164200/1‑148 (MQ=255)                                                                                           aaGACGGGTTTGCACGTCGATACTCCTGCCGTACTCAAGGATTTCGTCGTGATGACGAAGGTGAAGCGC‑TGGGTCTGCCCAGGTCCAGAATTTTTCGCAGCGACATCTCATATCAATCTCCTCTTACTTATCCCATTAGGCGCTGTaaa                                          <  6:303030/149‑1 (MQ=255)                                                                                             gACGGGTTTGCACGTCGATACTCCTGCCGTCCTCAAGGATTTCGTCGTGATGACGAAGGTGAAGCGC‑TGGGTCTGCCCAGGTCCAGAATTTTTCGCCGCGACATCTCATATCAATCTCCTCTTACTTATCCCAGTAGGCGCGGTAAaga                                        <  3:288403/149‑1 (MQ=255)                                                                                                 ggTTTGCACGTCGATACTCCTGCCGTCCTCAAGGATTTCGTCGTGATGACGAAGGTGAAGCGC‑TGGGGCTGCCCAGGTCCAGAATTTTTCGCCGCGACATCTCATATCAATCTCCTCTTACTTATCCCAGTAGGCGCGGTAAAGAGAgg                                    <  1:144864/149‑1 (MQ=255)                                                                                                     tGCACGTCGATACTCCTGCCGTCCTCAAGGATTTCGTCGTGATGACGAAGGTGAAGCGC‑TGGGTCTGCCCAGGTCCAGAATTTTTCGCCGCGACATCTCATATCAATCTCCTCTTACTTATCCCAGTAGGCGCGGTAAAGAGAGGgat                                 <  4:89831/148‑1 (MQ=255)                                                                                                                   ccTGCCGTCCTCAAGGATTTCGTCGTGATGACGAAGGTGAAGCGC‑TGGGTCTGCCCAGGTCCAGAATTTTTCGCCGCGACATCTCATATCAATCTCCTCTTACTTATCCCAGTAGGCGCGGTAAagaga                                      >  2:273109/1‑129 (MQ=255)                                                                                                                   ccTGCCGTCCTCAAGGATTTCGTCGTGATGACGAAGGTGAAGCGC‑TGGGTCTGCCCAGGTCCAGAATTTTTCGCCGCGACATCTCATATCAATCTCCTCTTACTTATCCCAGTAGGCGCGGTAAagaga                                      <  1:273109/129‑1 (MQ=255)                                                                                                                    cTGCCGTCCTCAAGGATTTCGTCGTGATGACGAAGGTGAAGCGC‑TGGGTCTGCCCAGGTACAGAATTTTTCGCCGCGACATCTCATATCAATCTCCTCTTACTTATCCCAGTAGGCGCGGTAAAGAGAGGGATAGATATCCATTTCGc                  <  5:102024/148‑1 (MQ=255)                                                                                                                    cTGCCGTCCTCAAGGATTTCGTCGTGATGACGAAGGTGAAGCGC‑TGGGTCTGCCCAGCTCCAGAATTTTTCGCCGCGACATCTCATATCAATCTCCTCTTACTTATCCCAGTAGGCGCGGTAAAGAGAGGGATAGATATCCATTTCGCt                 >  2:34990/1‑149 (MQ=255)                                                                                                                            cTCAAGGATTTCGTCGTGATGACGAAGGTGAAGCGC‑TGGGTCTGCCCAGGTCCAGAATTTTTCGCCGCGACATCTCATATCAATCTCCTCTTACTTATCCCAGTAGGCGCGGTAAAGAGAGGGATAGATATCCATTTCGCTTAAATGc          >  1:182230/1‑148 (MQ=255)                                                                                                                                   ccttCGTCATCACGACGAAGGTGAAGCGC‑TGGGTCTGCCCAGGTCCAGAATTTTTCGCCGCGACATCTCATATCAATCTCCTCTTACTTATCCCAGTAGGCGCGGTAAAGAGAGGGATAGATATCCATTTCGCTTAAATGCGACCGGTg  >  6:191692/3‑149 (MQ=255)                                                                                                                                               |                                                                                                                                          GCTTGGTCTGGTGCTGTAAGCCTCTTCTACAATTCGGTCCCCGCTTTTGGAGTACACCCCGATGAAGAGCTGCGTTTCGCCTGTCCGCGAAAGACGGGTTTGCACGTCGATACTCCTGCCGTCCTCAAGGATTTCGTCGTGATGACGAAGGTGAAGCGC‑TGGGTCTGCCCAGGTCCAGAATTTTTCGCCGCGACATCTCATATCAATCTCCTCTTACTTATCCCAGTAGGCGCGGTAAAGAGAGGGATAGATATCCATTTCGCTTAAATGCGACCGGTG  >  NC_002947/4424742‑4425020

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: ‑