Predicted mutation
evidence	seq id	position	mutation	freq	annotation	gene	description
RA	NC_002947	1,388,057	A→C	9.5%	S147A (TCC→GCC)	PP_1209 ←	cold‑shock protein

Read alignment evidence...
	seq id	position		ref	new	freq	score (cons/poly)	reads	annotation	genes	product
*	NC_002947	1,388,057	0	A	C	9.5%	103.9 / 3.2	42	S147A (TCC→GCC)	PP_1209	cold‑shock protein
Reads supporting (aligned to +/- strand):  ref base A (20/18);  new base C (2/2);  total (22/20)
Fisher's exact test for biased strand distribution p-value = 1.00e+00
Kolmogorov-Smirnov test that lower quality scores support variant p-value = 6.66e-01

GGTTTACTGCAACCACGTCTTCGGCCTGCAGGCCCTTGTCGCGGTGCATCACCG‑AAAACTCCACGCGCTGGCCTTCGACCAGAATGCGGTGGCCCTCACCGCG‑GATGGCCCGAAAGTGCACGAAGATGTCATCGCCCGAGTCTCGGGAGATGAAACCAAAGCCTTTCGACGTGTTGAACCATTTGACGGTGCCGGTATCACGGTTGCCGGCATCTTGTGCCACGTGTTGAGTGCCGCGTGCCTTGCGCGTGCTGCGGGCAAAGCCCACGGCCAGATGCACGGCCACGGCCA  >  NC_002947/1387910‑1388200                                                                                                                                                      |                                                                                                                                                ggTTTACTGCAACCACGTCTTCGGCCTGCAGGCCCTTGTCGCTGTGCATCACCG‑AAAACTCCACGCGCTGGCCTTCGACCAGAATGCGGTGGCCCTCACCGCG‑GATGGCCCGAAAGTGCACGAAGATGTCATCGCCCGAGTCTCGGgaga                                                                                                                                               <  1:269323/150‑1 (MQ=255)        tGCAACCACGTCTTCGGCCTGCAGGCCCTTGTCGCGGTGCATCACCG‑AAAACTCCACGCGCTGGCCTTCGACCAGAATGCGGTGGCCCTCACCGCG‑GATGGCCCGAAAGTGCACGAAGATGTCATCGCCCGAGTCTCGGGAGATGAAAcc                                                                                                                                        >  2:118556/1‑150 (MQ=255)             ccACGTCTTCGGCCTGCAGGCCCTTGTCGCGGTGCATCACCG‑AAAACTCCACGCGCTGGCCTTCGACCAGAATGCGGTGGCCCTCACCGCG‑GATGGCCCGAAAGTGCACGAAGATGTCATCGCCCGAGTCTCGGGAGATGaaa                                                                                                                                          <  1:596017/143‑1 (MQ=255)             caaCGTCTTCGGCCTGCAGGCCCTTGTCGCGGTGCATCACCG‑AAAACTCCACGCGCTGGCCTTCGACCAGAATGCGGTGGCCCTCACCGCG‑GATGGCCCGAAAGTGCACGAAGATGTCATCGCCCGAGTCTCGGGAGATGaaa                                                                                                                                          >  2:596017/3‑143 (MQ=255)              cACGTCTTCGGCCTGCAGGCCCTTGTCGCGGTGCATCACCG‑AAAACTCCACGCGCTGGCCTTCGACCAGAATGCGGTGGCCCTCACCGCG‑GATGGCCCGAAAGTGCACGAAGATGTCATCGCCCGAGTCTCGGGAGATGAAACCAAAGcc                                                                                                                                  >  1:82757/1‑150 (MQ=255)                cGTCTTCGGCCTGCAGGCCCTTGTCGCGGTGCATCACCG‑AAAACTCCACGCGCTGGCCTTCGACCAGAATGCGGTGGCCCTCACCGCG‑GATGGCCCGAAAGTGCACGAAGATGTCATCGCCCGAGTCTCGGGAGATGAAACCAAAGCCtt                                                                                                                                >  2:745855/1‑150 (MQ=255)                cGTCTTCGGCCTGCAGGCCCTTGTCGCGGTGCATCACCG‑AAAACTCCACGCGCTGGCCTTCGACCAGAATGCGGTGGAATTGACTGCG‑GATGGCCCGAAAGTGCACGAAGATGTCATCGCCCGAGGCTCGGGAGGTGAAACCAAAGCCtt                                                                                                                                >  1:535817/1‑150 (MQ=255)                 gTCTTCGGCCTGCAGGCCCTTGTCGCGGTGCATCACCG‑AAAACTCCACGCGCTGGCCTTCGACCAGAATGCGGTGGCCCTCACCGCG‑GATGGCCCGAAAGTGCACGAAGATGTCATCGCCCGAGTCTCGGGAGATGAAACCAAAGCCttt                                                                                                                               <  1:348214/150‑1 (MQ=255)                  tCTTCGGCCTGCAGGCCCTTGTCGCGGTGCATCACCG‑AAAACTCCACGCGCTGGCCTTCGACCAGAATGCCGTGGCCCTCACCGCG‑GATGGCCCGAAAGTGCACGAAGATGTCATCGCCCGAGTCTCGGGAGATGAAACCAAAGCCTTTc                                                                                                                              <  1:572898/150‑1 (MQ=255)                    ttCGGCCTGCAGGCCCTTGTCGCGGTGCATCACCG‑AAAACTCCACGCGCTGGCCTTCGACCAGAATGCGGTGGCCCTCACCGCG‑GATGGCCCGAAAGTGCACGAAGATGTCATCTCCCGAGACTCGGGCGAt                                                                                                                                              <  1:381232/132‑1 (MQ=255)                    ttCGGCCTGCAGGCCCTTGTCGCGGTGCATCACCG‑AAAACTCCACGCGCTGGCCTTCGACCAGAATGCGGTGGCCCTCACCGCG‑GATGGCCCGAAAGTGCACGAAGATGTCATCTCCCGAGACTCGGGCGAt                                                                                                                                              >  2:381232/1‑132 (MQ=255)                    ttCGGCCTGCAGGCCCTTGTCGCGGTGCATCACCG‑AAAACTCCACGCGCTGGCCTTCGACCAGAATGCGGTGGCCCTCACCGCG‑GATGGCCCGAAAGTGCACGAAGATGTCATCGCCCGAGTCTCGGGAGATGAAACCAAAGCCTTTCGa                                                                                                                            >  2:119874/1‑150 (MQ=255)                          cTGCAGGCCCTTGTCGCGGTGC‑CCACCGTAAAACTCCACGCGCTGGCCTTCGACCAGAATGCGGTGGCCCTCACCGCG‑GATTGCCCGAAAGTGCACGAAGATGTCATCGCCCGAGTCTCGGGAGATGAAACCAAAGCCTTTCGACGTGtt                                                                                                                      >  1:706763/1‑150 (MQ=255)                                gCCCTTGTCGCGGTGCATCACCG‑AAAACTCCACGCGCTGGCCTTCGACCAGAATGCGGTGGCCCTCACCGCG‑GATGGCCCGAAAGTGCACGAAGATGTCATCGCCCGAGTCTCGGGAGATGAAACCAAAGCCTTTCGACGTGTTGAACCa                                                                                                                <  2:164077/150‑1 (MQ=255)                                      gTCGCGGTGCATCACCG‑AAAACTCCACGCGCTGGCCTTCGACCAGAATGCGGTGGCCCTCACCGCG‑GATGGCCCGAAAGTGCACGAAGATGTCATCGCCCGAGTCTCGGGAGATGAAACCAAAGCCTTTCGACGTGTTGAACCATTTgcc                                                                                                          <  2:610390/150‑3 (MQ=255)                                              gCATCACCG‑AAAACTCCCCGCGCTGGCCTTCGACCAGAATGCGGTGGCCCT‑AGCGAGTTGTGGTCCGAAAGTGCACGAAGATGTCATCGCCCGAGTCTCGGGAGATGAAACCAAAGCCTTTCGACGTGTTGAACCATTTGACGGTGCCgg                                                                                                  <  2:706763/150‑1 (MQ=255)                                                   aCCG‑AAAACTCCACGCGCTGGCCTTCGACCAGAATGCGGTGGCCCTCACCGCG‑GATGGCCCGAAAGTGCACGAAGATGTCATCGCCCGAGTCTCGGGAGATGAAACCAAAGCCTTTCGACGTGTTGAACCATTTGACGGTGCCGGTATCa                                                                                             <  1:123789/150‑1 (MQ=255)                                                     cG‑AAAACTCCACGCGCTGGCCTTCGACCAGAATGCGGTGGCCCTCACCGCG‑GATGGCCCGAAAGTGCACGAAGATGTCATCTCCCGAGACTCGGgcga                                                                                                                                               <  1:387937/98‑1 (MQ=255)                                                             tCCACGCGCTGGCCTTCGACCAGAATGCGGTGGCCCTCACCGCG‑GATGGCCCGAAAGTGCACGAAGATGTCATCGCCCGAGTCTCGGGAGATGAAACCAAAGCCTTTCGACGTGTTGAACCATTTGACGGTGCCGGTATCa                                                                                             >  2:388998/1‑141 (MQ=255)                                                             tCCACGCGCTGGCCTTCGACCAGAATGCGGTGGCCCTCACCGCG‑GATGGCCCGAAAGTGCACGAAGATGTCATCGCCCGAGTCTCGGGAGATGAAACCAAAGCCTTTCGACGTGTTGAACCATTTGACGGTGCCGGTATCa                                                                                             <  1:388998/141‑1 (MQ=255)                                                             tCCACGCGCTGGCCTTCGACCAGAATGCGGTGGCCCTCACCGCG‑GATGGCCCGAAAGTGCACGAAGATGTCATCGCCCGAGTCTCGGGAGATGAAACCAAAGCCTTTCGACGTGTTGAACCATTTGACGGTGCCGGTATCACGGTTGCCg                                                                                    >  1:357149/1‑150 (MQ=255)                                                             tCCACGCGCTGGCCTTCGACCAGAATGCGGTGGCCCTCACCGCG‑GATGGCCCGAAAGTGCACGAAGATGTCATCGCCCGAGTCTCGGGAGATGAAACCAAAGCCTTTCGACGTGTTGAACCATTTGACGGTGCCGGTATCACGGTTGCCg                                                                                    >  1:97597/1‑150 (MQ=255)                                                                    gcTGGCCTTCGACCAGAATGCGGTGGCCCTCACCGCG‑GATGGCCCGAAAGTGCACGAAGATGTCATCTCCCGAGACTCGGGCGAt                                                                                                                                              <  2:726470/85‑1 (MQ=39)                                                                    gcTGGCCTTCGACCAGAATGCGGTGGCCCTCACCGCG‑GATGGCCCGAAAGTGCACGAAGATGTCATCTCCCGAGACTCGGGCGAt                                                                                                                                              >  1:726470/1‑85 (MQ=39)                                                                      tGGCCTTCGACCAGAATGCGGTGGCCCTCACCGCG‑GATGGCCCGAAAGTGCACGAAGATGTCATCGCCCGAGTCTCGGGAGATGAAACCAAAGCCTTTCGACGTGTTGAACCATTTGACGGTGCCGGTATCACGGTTGCCGGCATCTtgt                                                                           <  2:82757/150‑1 (MQ=255)                                                                      tGGCCTTCGACCAGAATGCGGTGGCCCTCACCGCG‑GATGGCCCGAAAGAGCACGAAGATGTCATCGCCCGAGTCTCGGGAGATGAAACCAAAGCCTTTCGACGTGTTGAACCATTTGACGGTGCCGGTATCACGGTTGCCGGCATCTtgt                                                                           <  2:535817/150‑1 (MQ=255)                                                                           ttCGACCAGAATGCGGTGGCCCTCACCGCG‑GATGGCCCGAAAGTGCACGAAGATGTCATCGCCCGAGTCTCGGGAGATGAAACCAAAGCCTTTCGACGTGTTGAACCATTTGACGGTGCCGGTATCACGGTTGCCGGCATCTTGTGCCAc                                                                      >  1:339087/1‑150 (MQ=255)                                                                                ccAGAATGCGGTGGCCCTCACCGCG‑GATGGCCCGAAAGTGCACGAAGATGTCATCGCCCGAGTCTCGGGAGATGAAACCAAAGCCTTTCGACGTGTTGAACCATTTGACGGTGCCGGTATCACGGTTGCCGGCATCTTGTGCCACGTGtt                                                                 <  1:709716/150‑1 (MQ=255)                                                                                    aaTGCGGTGGCCCTCACCGCG‑GATGGCCCGAAAGTGCACGAAGATGTCATCGCCCGAGTCTCGGGAGATGAAACCAAAGCCTTTCGACGTGTTGAACCATTTGACGGTGCCGGTATCACGGTTGCCGGCATCTTGTGCCACGTGTTGAGt                                                             >  2:505636/1‑150 (MQ=255)                                                                                                cTCACCGCG‑GATGGCCCGAAAGTGCACGAAGATGTCATCGCCCGAGTCTCGGGAGATGAAACCAAAGCCTTTCGACGTGTTGAACCATTTGACGGTGCCGGTATCACGGTTGCCGGCATCTTGTGCCACGTGTTGAGTGCCGCGTGCCtt                                                 <  1:505636/150‑1 (MQ=255)                                                                                                       cg‑GATGGCCCGAAAGTGCACGAAGATGTCATCGCCCGAGTCTCGGGAGATGAAACCAAAGCCTTTCGACGTGTTGAACCATTTGACGGTGCCGGTATCACGGTTGCCGGCATCTTGTGCCACGTGTTGAGTGCCGCGTGCCTTGCGCGtg                                          <  2:505857/150‑1 (MQ=255)                                                                                                       cg‑GATGGCCCGAAAGTGCACGAAGATGTCATCGCCCGAGTCTCGGGAGATGAAACCAAAGCCTTTCGACGTGTTGAACCATTTGACGGTGCCGGTATCACGGTTGCCGGCATCTTGTGCCACGTGTTGAGTGCCGCGTGCCTTGCGCGtg                                          >  1:505857/1‑150 (MQ=255)                                                                                                          gATGGCCCGAAAGTGCACGAAGATGTCATCGCCCGAGTCTCGGGAGATGAAACCAAAGCCTTTCGACGTGTTGAACCATTTGACGGTGCCGGTATCACGGTTGCCGGCATCTTGTGCCACGTGTTGAGTGCCGCGTGCCTTGCGCGtgct                                        <  1:118556/150‑1 (MQ=255)                                                                                                               cccGAAAGTGCACGAAGATGTCATCGCCCGAGTCTCGGGAGATGAAACCAAAGCCttt                                                                                                                               >  1:32066/1‑58 (MQ=255)                                                                                                               cccGAAAGTGCACGAAGATGTCATCGCCCGAGTCTCGGGAGATGAAACCAAAGCCttt                                                                                                                               <  2:32066/58‑1 (MQ=255)                                                                                                                ccGAAAGTGCACGAAGATGTCATCGCCCGAGTCTCGGGAGATGAAACCAAAGCCTTTCGACGTGTTGAACCATTTGACGGTGCCGGTATCACGGTTGCCGGCATCTTGTGCCACGTGTTGAGTGCCGCGTGCCTTGCGCGTGCTGCGGGc                                  >  2:405444/1‑150 (MQ=255)                                                                                                                   aaaGTGCACGAAGATGTCATCGCCCGAGTCTCGGGAGATGAAACCAAAGCCTTTCGACGTGTTGAACCATTTGACGGTGCCGGTATCACGGTTGCCGGCATCTTGTGCCACGTGTTGAGTGCCGCGTGCCTTgc                                               >  2:244934/1‑134 (MQ=255)                                                                                                                   aaaGTGCACGAAGATGTCATCGCCCGAGTCTCGGGAGATGAAACCAAAGCCTTTCGACGTGTTGAACCATTTGACGGTGCCGGTATCACGGTTGCCGGCATCTTGTGCCACGTGTTGAGTGCCGCGTGCCTTgc                                               <  1:244934/134‑1 (MQ=255)                                                                                                                          aCGAAGATGTCATCGCCCGAGTCTCGGGAGATGAAACCAAAGCCTTTCGACGTGTTGAACCATTTGACGGTGCCGGTATCACGGTTGCCGGCATCtt                                                                             <  2:234647/97‑1 (MQ=255)                                                                                                                          aCGAAGATGTCATCGCCCGAGTCTCGGGAGATGAAACCAAAGCCTTTCGACGTGTTGAACCATTTGACGGTGCCGGTATCACGGTTGCCGGCATCtt                                                                             >  1:234647/1‑97 (MQ=255)                                                                                                                            gAAGATGTCATCGCCCGAGTCTCGGGAGATGAAACCAAAGCCTTTCGACGTGTTGAACCATTTGACGGTGCCGGTATCACGGTTGCCGGCATCTTGTGCCACGTGTTGAGTGCCGCGTGCCTTGCGCGTGCTGCGGGCAAAGCCCACGGc                      >  2:256277/1‑150 (MQ=255)                                                                                                                             aaGATGTCATCGCCCGAGTCTCGGGAGATGAAACCAAAGCCTTTCGACGTGTTGAACCATTTGACGGTGCCGGTATCACGGTTGCCGGCATCTTGTGCCACGTGTTGAGTGCCGCGTGCCTTGCGCGTGCTGCGGGCAAAGCCCACGGcc                     >  2:242437/1‑150 (MQ=255)                                                                                                                                     aTCGCCCGAGTCTCGGGAGATGAAACCAAAGCCTTTCGACGTGTTGAACCATTTGACGGTGCCGGTATCACGGTTGCCGGCATCTTGTGCCACGTGTTGAGTGCCGCGTGCCTTGCGCGTGCTGCGGGCAAAGCCCACGGCCAGATGcac             >  2:413851/1‑150 (MQ=255)                                                                                                                                                ctcGGGAGATGAAACCAAAGCCTTTCGACGTGTTGAACCATTTGACGGTGCCGGTATCACGGTTGCCGGCATCTTGTGCCACGTGTTGAGTGCCGCGTGCCTTGCGCGTGCTGCGGGCAAAGCCCACGGCCAGATGCAcggccacggcca  <  1:119874/150‑1 (MQ=255)                                                                                                                                                      agaTGAAACCAAAGCCTTTCGACGTGTTGAACCATTTGACGGTGCCGGTATCACGGTTGCCGGCATCTTGTGCCACGTGTTGAGTGCCGCGTGCCTTGCGCGTGCTGCGGGCAAAGCCCACGGCCAGATGcacgg           <  1:629126/135‑1 (MQ=255)                                                                                                                                                      |                                                                                                                                                GGTTTACTGCAACCACGTCTTCGGCCTGCAGGCCCTTGTCGCGGTGCATCACCG‑AAAACTCCACGCGCTGGCCTTCGACCAGAATGCGGTGGCCCTCACCGCG‑GATGGCCCGAAAGTGCACGAAGATGTCATCGCCCGAGTCTCGGGAGATGAAACCAAAGCCTTTCGACGTGTTGAACCATTTGACGGTGCCGGTATCACGGTTGCCGGCATCTTGTGCCACGTGTTGAGTGCCGCGTGCCTTGCGCGTGCTGCGGGCAAAGCCCACGGCCAGATGCACGGCCACGGCCA  >  NC_002947/1387910‑1388200

Alignment Legend
Aligned base mismatch/match (shaded by quality score): ATCG/ATCG < 3 ≤ ATCG/ATCG < 22 ≤ ATCG/ATCG < 32 ≤ ATCG/ATCG < 41 ≤ ATCG/ATCG
Unaligned base: atcg    Masked matching base: atcg    Alignment gap: ‑    Deleted base: ‑