Predicted mutation
evidence	seq id	position	mutation	freq	annotation	gene	description
RA	NC_002947	4,295,000	G→T	17.1%	S139S (TCC→TCA)	opdN ←	outer‑membrane porin D

Read alignment evidence...
	seq id	position		ref	new	freq	score (cons/poly)	reads	annotation	genes	product
*	NC_002947	4,295,000	0	G	T	17.1%	68.3 / 3.4	28	S139S (TCC→TCA)	opdN	outer‑membrane porin D
Reads supporting (aligned to +/- strand):  ref base G (10/13);  new base T (2/3);  total (12/16)
Fisher's exact test for biased strand distribution p-value = 1.00e+00
Kolmogorov-Smirnov test that lower quality scores support variant p-value = 1.00e+00

CCAGGGTGAACTTCAGGTCGTGCAGTTCTTCAGAGGTGAGCATGGCCCCATGGAACAGGGTCGGCAGCAGACGGCCATCGTTGTACTTGAGCAACGGCACATCCGGCATCATCGAACCGTACTTGAGCACGGTATTGGACACCTTGACCTTGGCCGCCAGGCCCATCTTCGCATACTGGTCGGCCGAGCGCCGGGGGTCGTGGCCAGACGAGGGCAGCAATCCACTGTTGCTGTCGGCCGGGCTGGAATCCAGTTTGAAGCCGAACATGCCCA  >  NC_002947/4294864‑4295136                                                                                                                                         |                                                                                                                                         ccAGGGTGAACTTCAGGTCGTGCAGTTCTTCAGAGGTGAGCATGGCCCCATGGAACAGGGTCGGCAGCAGACGGCCATCGTTGTACTTGAGCAACGGCACATCCGGCATCATCGAACCGTACTTGAGCACGGTATTGGACaccttgacct                                                                                                                             >  2:225311/1‑150 (MQ=255)   aGGGTGAACTTCAGGTCGTGCAGTTCTTCAGAGGTGAGCATGGCCCCATGGAACAGGGTCGGCAGAAGACGGCCCCAACAGTACTTGCGCAAGAGCATTCCGGGCATCATCGAACCGTACTTGAGCACGGTATTGGACaccttgaccttg                                                                                                                           <  1:1052810/150‑1 (MQ=255)            ttCAGGTCGTGCAGTTCTTCAGAGGTGAGCATGGCCCCATGGAACAGGGTCGGCAGCAGACGGCCATCGTTGTACTTGAGCAACGGCACATCCGGCATCATCGAACCGTACTTGAGCACGGTATTGGACACCTTGACCTTGGCCGCCAgg                                                                                                                  >  2:928677/1‑150 (MQ=255)             tCAGGTCGTGCAGTTCTTCAGAGGTGAGCATGGCCCCATGGAACAGGGTCGGCAGCAGACGGCCATCGTTGTACTTGAGCAACGGCACATCCGGCATCATCGAACCGTACTTGAGCACGGTATTGGACACCTTGACCTTGGCCGCCAGGc                                                                                                                 <  1:732120/150‑1 (MQ=255)                      gCAGTTCTTCAGAGGTGAGCATGGCCCCATGGAACAGGGTCGGCAGCAGACGGCCATCGTTGTACTTGAGCAACGGCACATCCGGCATCATCGAACCGTACTTGAGCACGGTATTGGACACCTTGACCTTGGCCGCCAGGCCCATCTTCg                                                                                                        >  2:705881/1‑150 (MQ=255)                       cAGTTCTTCAGAGGTGAGCATGGCCCCATGGAACAGGGTCGGCAGCAGACGGCCATCGTTGTACTTGAGCAACGGCACATCCGGCATCATCGAACCGTACTTGAGCACGGTATTGGACACCTTGACCTTGGCCGCCAGGCCCATCTTCGc                                                                                                       <  1:489366/150‑1 (MQ=255)                                agagGTGAGCATGGCCCCATGGAACAGGGTCGGCAGCAGACGGCCATCGTTGTACTTGAGCAACGGCACATCCGGCATCATCGAACCGTACTTGAGCACGGTATTGGACACCTTGACCTTGGCCGCCAGGCCCATCTTCGCATACTGGTc                                                                                              <  2:1024607/150‑1 (MQ=255)                                agagGTGAGCATGGCCCCATGGAACAGGGTCGGCAGCAGACGGCCATCGTTGTACTTGAGCAACGGCACATCCGGCATCATCGAACCGTACTTGAGCACGGTATTGGACACCTTGACCTTGGCCGCCAGGCCCATCTTCGCATACTGGTc                                                                                              <  1:874453/150‑1 (MQ=255)                                 gagGTGAGCATGGCCCCATGGAACAGGGTCGGCAGCAGACGGCCATCGTTGTACTTGAGCAACGGCACATCCGGCATCATCGAACCGTACTTGAGCACGGTATTGGACACCTTGACCTTGGCCGCCAGGCCCATCTTCGCATACTGGTCg                                                                                             <  1:705881/150‑1 (MQ=255)                                                         aGGGTCGGCAGCAGACGGCCATCGTTGTACTTGAGCAACGGCACATCCGGCATCATCGAACCGTACTTGAGCACGGTATTGGACACCTTGACCTTGGCCCAGAGGCCCATCTTCGCATACTGGTCGGCCGAGCGCCGGGGGTCGTGGCCa                                                                     <  1:879668/150‑1 (MQ=255)                                                           ggTCGGCAGCAGACGGCCATCGTTGTACTTGAGCAACGGCACATCCGCGATATTCGGGGTGCACTTGAGCACGGTATTGGACACCTTGACCTTGGCCGCCAGGCCCATCTTCGCATACTGGTCGGCCGAGCGCCGGGGGTCGTGGCCAGa                                                                   >  2:296553/1‑150 (MQ=255)                                                                  agcagACGGCCATCGTTGTACTTGAGCAACGGCACATCCGGCATCATCGAACCGTACTTGAGCACGGTATGTGACACCTTGACCTTGGCCGCCAGGCCCATCTTCGCATACTGGTCGGCCGAGCGCCGGGGGTCGTGGCCAGACGAGGgc                                                            >  1:989936/1‑150 (MQ=255)                                                                                 ttGTACTTGAGCAACGGCACATCCGGCATCATCGAACCGTACTTGAGCACGGTATTGGACACCTTGACCTTGGCCGCCAGGCCCATCTTCGCATACTGGTCGGCCGAGCGCCGGGGGTCGTGGCCAGACGAGGGCAGCAATCCACTGTTg                                             <  2:208156/150‑1 (MQ=255)                                                                                 ttGTACTTGACCAAAGGCAAACCCCGACTCATCGAACCGTACTTGAGCACGGGATTGGACACCTTGACCTGGGCCGCCAGGCCCATCTTCGCATACTGGTCGGCCGAGCGCCGGGGGTCGTGGCCAGACGAGGGCAGCAATCCACTGTTg                                             >  2:919664/1‑150 (MQ=255)                                                                                   gTACTTGAGCAACGGCACATCCGGCATCATCGAACCGTACTTGAGCAAGGTATTGGACACCTTGACCTTGGCCGCCAGGCCCATCTTCGCATACTGGTCGGCCGAGCGCCGGGGGTCGTGGCCAGACGAGGGCAGCAATCCACTGTTGCt                                           <  1:121893/150‑1 (MQ=255)                                                                                             aaCGGCACATCCGGCATCATCGAACCGTACTTGAGCACGGTATTGGACACCTTGACCTTGGCCGCCAGGCCCATCTTCGCATACTGGTCGGCCGAGCGCCGGGGGTCGTGGCCAGACGAGGGCAGCAATCCACTGTTGCTGTCGGCCggg                                 <  2:22176/150‑1 (MQ=255)                                                                                                ggCACATCCGGCATCATCGAACCGTACTTGAGCACGGTATTTGACACCTTGACCTTGGCCGCCAGGCCCATCTTCGCATACTGGTCGGCCGAGCGCCGGGGGTCGTGGCCAGACGAGGGCAGCAATCCACTGTTGCTGTCGGCCGGGCTg                              <  2:989936/150‑1 (MQ=255)                                                                                                 gCACATCCGGCATCATCGAACCGTACTTGAGCACGGTATTGGACACCTTGACCTTGGCCGCCAGGCCCATCTTAGCATACTGGTCGGCCGAGCGCCGGGGGCCGTTTCCTTACGGTTGCAGCAATCCACTGTTGCTGTCGGCCGGGCTgg                             >  1:270321/1‑150 (MQ=255)                                                                                                             tcatcGAACCGTACTTGAGCACGGTATTGGACACCTTGACCTTGGCCGCCAGGCCCATCTTCGCATACTGGTCGGCCGAGCGCCGGGGGTCGTGGCCAGACGAGGGCAGCAATCCACTGTTGCTGTCGGCCGGGCTGGAATCCAGTTTGa                 >  2:589154/1‑150 (MQ=255)                                                                                                              catcGAGCCGTTCTTGAGCACGGTGATTACGACCGTGGCCTGGGCCAGCAGGCCCATCTCCGGGTCATCAGCGGCGGAGCGCCGGGGGTCGTGGCCAGACGAGGGCAGCAATCCACTGTTGCTGTCGGCCGGGCTGGAATCCAGTTTGaa                <  1:928677/150‑1 (MQ=255)                                                                                                                   aaCCGTACTTGAGCACGGTATTGGACACCTTGACCTTGGCCGCCAGGCCCATCTTCGCATACTGGTCGGCCGAGCGCCGGGGGTCGTGGCCAGACGAGGGCAGCAATCCACTGTTGCTGTCGGCCGGGCTGGAATCCAGtt                    >  2:66411/1‑141 (MQ=255)                                                                                                                   aaCCGTACTTGAGCACGGTATTGGACACCTTGACCTTGGCCGCCAGGCCCATCTTCGCATACTGGTCGGCCGAGCGCCGGGGGTCGTGGCCAGACGAGGGCAGCAATCCACTGTTGCTGTCGGCCGGGCTGGAATCCAGtt                    <  1:66411/141‑1 (MQ=255)                                                                                                                                cACGGTATTGGACACCTTGACCTTGGCCGCCAGGCCCATCTTCGCATACTGGTCGGCCGAGCGCCGGGGGTCGTGGCCAGAGGAGGGCAGCAATCCACTGtt                                              >  1:980731/1‑102 (MQ=255)                                                                                                                                cACGGTATTGGACACCTTGACCTTGGCCGCCAGGCCCATCTTCGCATACTGGTCGGCCGAGCGCCGGGGGTCGTGGCCAGACGAGGGCAGCAATCCAc                                                  <  2:201144/98‑1 (MQ=255)                                                                                                                                cACGGTATTGGACACCTTGACCTTGGCCGCCAGGCCCATCTTCGCATACTGGTCGGCCGAGCGCCGGGGGTCGTGGCCAGACGAGGGCAGCAATCCAc                                                  >  1:201144/1‑98 (MQ=255)                                                                                                                                cACGGTATTGGACACCTTGACCTTGGCCGCCAGGCCCATCTTCGCATACTGGTCGGCCGAGCGCCGGGGGTCGTGGCCAGACGAGGGCAGCAATCCACTGtt                                              <  2:980731/102‑1 (MQ=255)                                                                                                                                     tATTTGACACCTTGACCTTGGCCGCCAGGCCCATCTTCGCATACTGGTCGGCCGAGCGCCGGGGGTCGTGGCCAGACGAGGGCAGCAATCCACTGTTGCTGTCGGCCGGGCTGGAATCCAGTTTGAAGCCGAACATGCCCa  <  2:1045230/141‑1 (MQ=255)                                                                                                                                     tATTTGACACCTTGACCTTGGCCGCCAGGCCCATCTTCGCATACTGGTCGGCCGAGCGCCGGGGGTCGTGGCCAGACGAGGGCAGCAATCCACTGTTGCTGTCGGCCGGGCTGGAATCCAGTTTGAAGCCGAACATGCCCa  >  1:1045230/1‑141 (MQ=255)                                                                                                                                         |                                                                                                                                         CCAGGGTGAACTTCAGGTCGTGCAGTTCTTCAGAGGTGAGCATGGCCCCATGGAACAGGGTCGGCAGCAGACGGCCATCGTTGTACTTGAGCAACGGCACATCCGGCATCATCGAACCGTACTTGAGCACGGTATTGGACACCTTGACCTTGGCCGCCAGGCCCATCTTCGCATACTGGTCGGCCGAGCGCCGGGGGTCGTGGCCAGACGAGGGCAGCAATCCACTGTTGCTGTCGGCCGGGCTGGAATCCAGTTTGAAGCCGAACATGCCCA  >  NC_002947/4294864‑4295136

Alignment Legend
Aligned base mismatch/match (shaded by quality score): ATCG/ATCG < 3 ≤ ATCG/ATCG < 12 ≤ ATCG/ATCG < 22 ≤ ATCG/ATCG < 37 ≤ ATCG/ATCG < 41 ≤ ATCG/ATCG
Unaligned base: atcg    Masked matching base: atcg    Alignment gap: ‑    Deleted base: ‑