Predicted mutation
evidence	seq id	position	mutation	freq	annotation	gene	description
RA	NC_002947	554,197	A→G	20.1%	D45G (GAT→GGT)	rpsC →	30S ribosomal protein S3

Read alignment evidence...
	seq id	position		ref	new	freq	score (cons/poly)	reads	annotation	genes	product
*	NC_002947	554,197	0	A	G	20.1%	37.6 / 6.0	25	D45G (GAT→GGT)	rpsC	30S ribosomal protein S3
Reads supporting (aligned to +/- strand):  ref base A (10/10);  new base G (3/2);  total (13/12)
Fisher's exact test for biased strand distribution p-value = 1.00e+00
Kolmogorov-Smirnov test that lower quality scores support variant p-value = 3.75e-01

CATATCACTGTCAAGGTTGCGGACAAGTAACGGAGTCGATCAGATGGGTCAGAAAGTACATCCCACTGGCATTCGCCTGGGAATCGTCAAGGAGCACACCTCCGTCTGGTACGCAGACGGTGCTACTTACGCAGATTACCTGTTGAAGGATCTGAAAACGCGTGAGTACCTCCAAGACAAACTAAAAAGCGCGTCCGTAAGCCGTATCGATATTCATCGTCCGGCTCAAACTGCACGCATCACCATCCACACCGCTCGTCCCGGTATCGTTATCGGTAA  >  NC_002947/554048‑554326                                                                                                                                                      |                                                                                                                                  cATATCACTGTCAAGGTTGCGGACAAGTAACGGAGTCGATCAGATGGGTCAGAAAGTACATCCCACTGGCATTCGCCTGGGAATCGTCAAGGAGCACACCTCCGTCTGGTACGCAGACGGTGCTACTTACGCAGATTACCTGTTGAAGGa                                                                                                                                   >  1:482615/1‑150 (MQ=255) cATATCACTGTCAAGGTTGCGGACAAGTAACGGAGTCGATCAGATGGGTCAGAAAGTACATCCCACTGGCATTCGCCTGGGAATCGTCAAGGAGCACACCTCCGTCTGGTACGCAGACGGTGCTACTTACGCAGATTACCTGTTGAAGGa                                                                                                                                   >  1:73208/1‑150 (MQ=255)    atCACTGTCAAGGTTGCGGACAAGTAACGGAGTCGATCAGATGGGTCAGAAAGTACATCCCACTGGCATTCGCCTGGGAATCGTCAAGGAGCACACCTCCGTCTGGTACGCAGACGGTGCTACTTACGCAGATTACCTGTTGAAGGATCt                                                                                                                                <  2:482615/150‑1 (MQ=255)           tCAAGGTTGCGGACAAGTAACGGAGTCGATCAGATGGGTCAGAAAGTACATCCCACTGGCATTCGCCTGGGAATCGTCAAGGAGCACACCTCCGTCTGGTACGCAGACGGTGCTACTTACGCAGATTACCTGTTGAAGGGTCTGAAAAcg                                                                                                                         >  2:593582/1‑150 (MQ=255)             aaGGTTGCGGACAAGTAACGGAGTCGATCAGATGGGTCAGAAAGTACATCCCACTGGCATTCGCCTGGGAATCGTCAAGGAGCACACCTCCGTCTGGTACGCAGACGGTGCTACTTACGCAGATTACCTGTTGAAGGATCTGAAAAcgcg                                                                                                                       >  2:355292/1‑150 (MQ=255)                              aCGGATTCGATCAGATGGGTCAGAAAGTACATCCCACTGGCATTCGCCTGGGAATCGTCAAGGAGCACACCTCCGTCTGGTACGCAGACGGTGCTACTTACGCAGATTACCTGTTGAAGGATCTGAAAACGCGTGAGTACCTCCAAGACa                                                                                                      >  2:738610/1‑150 (MQ=255)                                 gattCGATCAGATGGGTCAGAAAGTACATCCCACTGGCATTCGCCTGGGAATCGTCAAGGAGCACACCTCCGTCTGGTACGCAGACGGTGCTACTTACGCAGATTACCTGTTGAAGGATCTGAAAACGCGTGAGTACCTCCAAGACAAAc                                                                                                   <  1:738610/147‑1 (MQ=255)                                       aTCAGATGGGTCAGAAAGTACATCCCACTGGCATTCGCCTGGGAATCGTCAAGGAGCACACCTCCGTCTGGTACGCAGACGGTGCTACTTACGCAGATTACCTGTTGAAGGATCTGAAAACGCGTGAGTACCTCCAAGACAAACTaaaaa                                                                                             <  2:73208/150‑1 (MQ=255)                                                 tCAGAAAGTACATCCCACTGGCATTCGCCTGGGAATCGTCAAGGAGCACACCTCCGTCTGGTACGCAGACGGTGCTACTTACGCAGATTACCTGTTGAAGGGTCTGAAAACGCGTGAGTACCTCCAAGACAAACTAAAAAGCGCGTCCGt                                                                                   >  2:445949/1‑150 (MQ=255)                                                 tCAGAAAGTACATCCCACTGGCATTCGCCTGGGAATCGTCAAGGAGCACACCTCCGTCTGGTACGCAGACGGTGCTACTTACGCAGATTACCTGTTGAAGGATCTGAAAACGCGTGAGTACCTCCAAGACAAACTAAAAAGCGCGTCCGt                                                                                   >  2:177765/1‑150 (MQ=255)                                                    gAAAGTACATCCCACTGGCATTCGCCTGGGAATCGTCAAGGAGCACACCTCCGTCTGGTACGCAGACGGTGCTACTTACGCAGATTACCTGTTGAAGGATCTGAAAACGCGTGAGTACCTCCAAGACAAACTAAAAAGCGCGTCCGTAAg                                                                                >  1:685670/1‑150 (MQ=255)                                                            aTCCCACTGGCATTCGCCTGGGAATCGTCAAGGAGCACACCTACGTCTGGTACGCAGCTGGTGCTACTTGCTCATGTGACCTTTTGAAGGATCTGAAAACGCGTGAGTACCTCCAAGACAAACTAAAAAGCGCGTCCGTAAGCCGTATCg                                                                        >  1:467629/1‑150 (MQ=255)                                                              cccACTGGCATTCGCCTGGGAATCGTCAAGGAGCACACCTCCGTCTGGTACGCAGACGGTGCTACTTACGCAGATTACCTGTTGAAGGGTCTGAAAACGCGTGAGTACCTCCAAGACAAACTAAAAAGCGCGTCCGTAAGCCGTATCGat                                                                      <  1:593582/150‑1 (MQ=255)                                                                       aTTCGCCTGGGAATCGTCAAGGAGCACACCTCCGTCTGGTACGCAGACGGTGCTACTTACGCAGATTACCTGTTGAAGGATCTGAAAACGCGt                                                                                                                      >  1:471131/1‑93 (MQ=255)                                                                       aTTCGCCTGGGAATCGTCAAGGAGCACACCTCCGTCTGGTACGCAGACGGTGCTACTTACGCAGATTACCTGTTGAAGGATCTGAAAACGCGt                                                                                                                      <  2:471131/93‑1 (MQ=255)                                                                            ccTGGGAATCGTCAAGGAGCACACCTCCGTCTGGTACGCAGACGGTGCTACTTACGCAGATTACCTGTTGAAGGATCTGAAAACGCGTGAGTACCTCCAAGACAAACTAAAAAGCGCGTCCGTAAGCCGTATCGATATTCATCGTCCGGc                                                        <  1:177765/150‑1 (MQ=255)                                                                              tGGGAATCGTCAAGGAGCACACCTCCGTCTGGTACGCAGACGGTGCTACTTACGCAGATTACCTGTTGAAGGATCTGAAAACGCGTGAGTACCGCCAAGACAAACTAAAAAGCGCGTCCGTAAGCCGTATCGATATTCATCGTCCGGCTc                                                      >  1:710867/1‑150 (MQ=255)                                                                                     cGTCAAGGAGCACACCTCCGTCTGGTACGCAGACGGTGCTACTTACGCAGATTACCTGTTGAAGGATCTGAAAACGCGTGAGTACCTCCAAGACAAACTAAAAAGCGCGTCCGTAAGCCGTATCGATATTCATCGTCCGGCTCAAACTGc                                               <  2:662883/150‑1 (MQ=255)                                                                                          aGGAGCACACCTCCGTCTGGTACGCAGACGGTGCTACTTACGCAGATTACCTGTTGAAGGATCTGAAAACGCGTGAGTACCTCCAAGACAAACTAAAAAGCGCGTCCGTAAGCCGTATCGATATTCATCGTCCg                                                          <  2:333140/134‑1 (MQ=255)                                                                                          aGGAGCACACCTCCGTCTGGTACGCAGACGGTGCTACTTACGCAGATTACCTGTTGAAGGATCTGAAAACGCGTGAGTACCTCCAAGACAAACTAAAAAGCGCGTCCGTAAGCCGTATCGATATTCATCGTCCg                                                          >  1:333140/1‑134 (MQ=255)                                                                                                   ccTCCGTCTGGTACGCAGACGGTGCTACTTACGCAGATTACCTGTTGAAGGATCTGAAAACGCGTGAGTACCTCCAAGACAAACTAAAAAGCGCGTCCGTAAGCCGTATCGATATTCATCGTCCGGCTCAAACTGCACGCATCACCATcc                                 >  2:64761/1‑150 (MQ=255)                                                                                                    cTCCGTCTGGTACGCAGACGGTGCTACTTACGCAGATTACCTGTTGAAGGATCTGAAAACGCGTGAGTACCTCCAAGACAAACTAAAAAGCGCGTCCGTAAGCCGTATCGATATTCATCGTCCGGCTCAAACTGCACGCATCACCATCca                                <  2:169921/150‑1 (MQ=255)                                                                                                     tCCGTCTGGTACGCAGACGGTGCTACTTACGCAGATTACCTGTTGAAGGATCTGAAAACGCGTGAGTACCTCCAAGACAAACTAAAAAGCGCGTCCGTAAGCCGTATCGATATTCATCGTCCGGCTCAAAc                                                  >  2:237682/1‑131 (MQ=255)                                                                                                     tCCGTCTGGTACGCAGACGGTGCTACTTACGCAGATTACCTGTTGAAGGATCTGAAAACGCGTGAGTACCTCCAAGACAAACTAAAAAGCGCGTCCGTAAGCCGTATCGATATTCATCGTCCGGCTCAAAc                                                  <  1:237682/131‑1 (MQ=255)                                                                                                               aCGCAGACGGTGCTACTTACGCAGATTACCTGTTGAAGGGTCTGAAAACGCGTGAGTACCTCCAAGACAAACTAAAAAGCGCGTCCGTAAGCCGTATCGATATTCATCGTCCGGCTCAAACTGCACGCATCACCATCCACACCGCTCGTc                     >  1:172825/1‑150 (MQ=255)                                                                                                                            tACTTACGCAGATTACCTGTTGAAGGGTCTGAAAACGCGTGAGTACCTCCAAGACAAACTAAAAAGCGCGTCCGTAAGCCGTATCGATATTCATCGTCCGGCTCAAACTGCACGCATCACCATCCACACCGCTCGTCCCGGTATCGTTAt        <  2:172825/150‑1 (MQ=255)                                                                                                                                  cGCAGATTACCTGTTGAAGGATCTGAAAACGCGTGAGTACCTCCAAGACAAACTAAAAAGCGCGTCCGTAAGCCGTATCGATATTCATCGTCCGGCTCAAACTGCACGCATCACCATCCACACCGCTCGTCCCGGTATCGTTATCGGTaa  <  2:467629/150‑1 (MQ=255)                                                                                                                                                      |                                                                                                                                  CATATCACTGTCAAGGTTGCGGACAAGTAACGGAGTCGATCAGATGGGTCAGAAAGTACATCCCACTGGCATTCGCCTGGGAATCGTCAAGGAGCACACCTCCGTCTGGTACGCAGACGGTGCTACTTACGCAGATTACCTGTTGAAGGATCTGAAAACGCGTGAGTACCTCCAAGACAAACTAAAAAGCGCGTCCGTAAGCCGTATCGATATTCATCGTCCGGCTCAAACTGCACGCATCACCATCCACACCGCTCGTCCCGGTATCGTTATCGGTAA  >  NC_002947/554048‑554326

Alignment Legend
Aligned base mismatch/match (shaded by quality score): ATCG/ATCG < 3 ≤ ATCG/ATCG < 12 ≤ ATCG/ATCG < 27 ≤ ATCG/ATCG < 37 ≤ ATCG/ATCG < 41 ≤ ATCG/ATCG
Unaligned base: atcg    Masked matching base: atcg    Alignment gap: ‑    Deleted base: ‑