Predicted mutation
evidence	seq id	position	mutation	annotation	gene	description
RA	NC_000913	2,957,222	G→A	R555C (CGT→TGT)	ptrA ←	protease 3

Read alignment evidence...
	seq id	position		ref	new	freq	score (cons/poly)	reads	annotation	genes	product
*	NC_000913	2,957,222	0	G	A	96.2%	81.4 / ‑4.2	26	R555C (CGT→TGT)	ptrA	protease 3
Reads supporting (aligned to +/- strand):  ref base G (1/0);  new base A (11/14);  total (12/14)
Fisher's exact test for biased strand distribution p-value = 4.62e-01
Kolmogorov-Smirnov test that lower quality scores support variant p-value = 9.97e-01

TTGTTAGCGTTGGTGGAAAAACTTATGCCACCAACCGACGCCTGGTTGCTTAACTGATCAAGCGCCAGCCCTGCGAGATAATCATTGAGCGCAAACATCACCTGATTGCGGGCGCTGTCCATGGCTTTCGGATTACGCAAAATCAGGCTGACATCAGCTTTGGGCTCGCTGGCAAAATAACGGCTTGGCGCATACACCACGCGCAGATTCGACTCATCAACAATCAGCTCTGGATGGTCGTATTTCTTCTCTGACTTAATCAGCGAG  >  NC_000913/2957086‑2957352                                                                                                                                         |                                                                                                                                   ttgttAGCGTTGGTGGAAAAACTTATGCCACCAACCGACGCCTGGTTGCTTAACTGATCAAGCGCCAGCCCTGCGAGATAATCATTGAGCGCAAACATCACCTGATTGCGGGCGCTGTCCATGGCTTTCGGATTACACaa                                                                                                                                 >  1:365040/1‑140 (MQ=255)        cGTTGGTGGAAAAACTTATGCCACCAACCGACGCCTGGTTGCTTAACTGATCAAGCGCCAGCCCTGCGAGATAATCATTGAGCGCAAACATCACCTGATTGCGGGCGCTGTCCATGGCTTTCGGATTACACAAAATCAgg                                                                                                                          <  1:311096/140‑1 (MQ=255)            ggtggAAAAACTTATGCCACCAACCGACGCCTGGTTGCTTAACTGATCAAGCGCCAGCCCTGCGAGATAATCATTGAGCGCAAACATCACCTGATTGCGGGCGCTGTCCATGGCTTTCGGATTACGCAAAATCAGGCTGa                                                                                                                      >  1:149915/1‑140 (MQ=255)            ggtggAAAAACTTATGCCACCAACCGACGCCTGGTTGCTTAACTGATCAAGCGCCAGCCCTGCGAGATAATCATTGAGCGCAAACATCACCTGATTGCGGGCGCTGTCCATGGCTTTCGGATTACACAAAATCAGGCTGa                                                                                                                      >  1:154859/1‑140 (MQ=255)              tggAAAAACTTATGCCACCAACCGACGCCTGGTTGCTTAACTGATCAAGCGCCAGCCCTGCGAGATAATCATTGAGCGCAAACATCACCTGATTGCGGGCGCTGTCCATGGCTTTCGGATTACACAAAATCAGGCTGCCa                                                                                                                    >  2:233419/1‑140 (MQ=255)                              accaACCGACGCCTGGTTGCTTAACTGATCAAGCGCCAGCCCTGCGAGATAATCATTGAGCGCAAACATCACCTGATTGCGGGCGCTGTCCATGGCTTTCGGATTACACAAAATCAGGCTGACATCAGCTTTGGGCTCGc                                                                                                    <  1:301672/140‑1 (MQ=255)                              accaACCGACGCCTGGTTGCTTAACTGATCAAGCGCCAGCCCTGCGAGATAATCATTGAGCGCAAACATCACCTGATTGCGGGCGCTGTCCATGGCTTTCGGATTACACAAAATCAGGCTGACATCAGCTTTGGGCTCGc                                                                                                    <  1:99600/140‑1 (MQ=255)                                             gTTGCTTAACTGATCAAGCGCCAGCCCTGCGAGATAATCATTGAGCGCAAACATCACCTGATTGCGGGCGCTGTCCATGGCTTTCGGATTACACAAAATCAGGCTGACATCAGCTTTGGGCTCGCTGGCAAAATAACGGc                                                                                     >  1:212221/1‑140 (MQ=255)                                               tGCTTAACTGATCAAGCGCCAGCCCTGCGAGATAATCATTGAGCGCAAACATCACCTGATTGCGGGCGCTGTCCATGGCTTTCGGATTACACAAAATCAGGCTGACATCAGCTTTGGGCTCGCTGGCAAAATAACGGCtt                                                                                   <  2:212221/140‑1 (MQ=255)                                                gCTTAACTGATCAAGCGCCAGCCCTGCGAGATAATCATTGAGCGCAAACATCACCTGATTGCGGGCGCTGTCCATGGCTTTCGGATTACACAAAATCAGGCTGACATCAGCTTTGGGCTCGCTGGCAAAATAACGGCTTg                                                                                  <  2:154859/140‑1 (MQ=255)                                                           cAAGCGCCAGCCCTGCGAGATAATCATTGAGCGCAAACATCACCTGATTGCGGGCGCTGTCCATGGCTTTCGGATTACACAAAATCAGGCTGACATCAGCTTTGGGCTCGCTGGCAAAATAACGGCTTGGCGCATAcacc                                                                       <  2:365040/140‑1 (MQ=255)                                                            aaGCGCCAGCCCTGCGAGATAATCATTGAGCGCAAACATCACCTGATTGCGGGCGCTGTCCATGGCTTTCGGATTACACAAAATCAGGCTGACATCAGCTTTGGGCTCGCTGGCAAAATAACGGCTTGGCGCATAcacca                                                                      <  2:127815/140‑1 (MQ=255)                                                                gcCAGCCCTGCGAGATAATCATTGAGCGCAAACATCACCTGATTGCGGGCGCTGTCCATGGCTTTCGGATTACACAAAATCAGGCTGACATCAGCTTTGGGCTCGCTGGCAAAATAACGGCTTGGCGCATACACCAcgcg                                                                  <  2:200715/140‑1 (MQ=255)                                                                                     ttGAGCGCAAACATCACCTGATTGCGGGCGCTGTCCATGGCTTTCGGATTACACAAAATCAGGCTGACATCAGCTTTGGGCTCGCTGGCAAAATAACGGCTTGGCGCATACACCACGCGCAGATTCGACTCATCAACAAt                                             <  1:233419/140‑1 (MQ=255)                                                                                       gAGCGCAAACATCACCTGATTGCGGGCGCTGTCCATGGCTTTCGGATTACACAAAATCAGGCTGACATCAGCTTTGGGCTCGCTGGCAAAATAACGGCTTGGCGCATACACCACGCGCAGATTCGACTCATCAACAATCa                                           >  2:1473/1‑140 (MQ=255)                                                                                        aGCGCAAACATCACCTGATTGCGGGCGCTGTCCATGGCTTTCGGATTACACAAAATCAGGCTGACATCAGCTTTGGGCTCGCTGGCAAAATAACGGCTTGGCGCATACACCACGCGCAGATTCGACTCATCAACAATCAg                                          <  2:75113/140‑1 (MQ=255)                                                                                          cgcAAACATCACCTGATTGCGGGCGCTGTCCATGGCTTTCGGATTACACAAAATCAGGCTGACATCAGCTTTGGGCTCGCTGGCAAAATAACGGCTTGGCGCATACACCACGCGCAGATTCGACTCATCAACAATCAGct                                        >  2:385310/1‑140 (MQ=255)                                                                                            cAAACATCACCTGATTGCGGGCGCTGTCCATGGCTTTCGGATTACACAAAATCAGGCTGACATCAGCTTTGGGCTCGCTGGCAAAATAACGGCTTGGCGCATACACCACGCGCAGATTCGACt                                                       <  1:216641/123‑1 (MQ=255)                                                                                            cAAACATCACCTGATTGCGGGCGCTGTCCATGGCTTTCGGATTACACAAAATCAGGCTGACATCAGCTTTGGGCTCGCTGGCAAAATAACGGCTTGGCGCATACACCACGCGCAGATTCGACt                                                       >  2:216641/1‑123 (MQ=255)                                                                                                     ccTGATTGCGGGCGCTGTCCATGGCTTTCGGATTACACAAAATCAGGCTGACATCAGCTTTGGGCTCGCTGGCAAAATAACGGCTTGGCGCATACACCACGCGCAGATTCGACTCATCAACAATCAGCTCTGGATGGTCg                             >  1:257890/1‑140 (MQ=255)                                                                                                         aTTGCGGGCGCTGTCCATGGCTTTCGGATTACACAAAATCAGGCTGACATCAGCTTTGGGCTCGCTGGCAAAATAACGGCTTGGCGCATACACCACGCGCAGATTCGACTCATCAACAATCAGCTCTGGATGGTCGTAtt                         >  2:48923/1‑140 (MQ=255)                                                                                                             cGGGCGCTGTCCATGGCTTTCGGATTACACAAAATCAGGCTGACATCAGCTTTGGGCTCGCTGGCAAAATAACGGCTTGGCGCATACACCACGCGCAGATTCGACTCATCAACAATCAGCTCTGGATGGTCGTATttctt                     >  2:173701/1‑140 (MQ=255)                                                                                                               ggCGCTGTCCATGGCTTTCGGATTACACAAAATCAGGCTGACATCAGCTTTGGGCTCGCTGGCAAAATAACGGCTTGGCGCATACACCACGCGCAGATTCGACTCATCAACAATCAGCTCTGGATGGTCGTATTtcttct                   <  1:385310/140‑1 (MQ=255)                                                                                                               ggCGCTGTCCATGGCTTTCGGATTACACAAAATCAGGCTGACATCAGCTTTGGGCTCGCTGGCAAAATAACGGCTTGGCGCATACACCACGCGCAGATTCGACTCATCAACAATCAGCTCTGGATGGTCGTATTtcttct                   <  2:257890/140‑1 (MQ=255)                                                                                                               ggCGCTGTCCATGGCTTTCGGATTACACAAAATCAGGCTGACATCAGCTTTGGGCTCGCTGGCAAAATAACGGCTTGGCGCATACACCACGCGCAGATTCGACTCATCAACAATCAGCTCTGGATGGTCGTATTtcttct                   <  1:1473/140‑1 (MQ=255)                                                                                                                                tCGGATTACACAAAATCAGGCTGACATCAGCTTTGGGCTCGCTGGCAAAATAACGGCTTGGCGCATACACCACGCGCAGATTCGACTCATCAACAATCAGCTCTGGATGGTCGTATTTCTTCTCTGACTTAATCAGCgag  >  1:156676/1‑140 (MQ=255)                                                                                                                                tCGGATTACACAAAATCAGGCTGACATCAGCTTTGGGCTCGCTGGCAAAATAACGGCTTGGCGCATACACCACGCGCAGATTCGACTCATCAACAATCAGCTCTGGATGGTCGTATTTCTTCTCTGACTTAATCAGCgag  >  1:127662/1‑140 (MQ=255)                                                                                                                                         |                                                                                                                                   TTGTTAGCGTTGGTGGAAAAACTTATGCCACCAACCGACGCCTGGTTGCTTAACTGATCAAGCGCCAGCCCTGCGAGATAATCATTGAGCGCAAACATCACCTGATTGCGGGCGCTGTCCATGGCTTTCGGATTACGCAAAATCAGGCTGACATCAGCTTTGGGCTCGCTGGCAAAATAACGGCTTGGCGCATACACCACGCGCAGATTCGACTCATCAACAATCAGCTCTGGATGGTCGTATTTCTTCTCTGACTTAATCAGCGAG  >  NC_000913/2957086‑2957352

Alignment Legend
Aligned base mismatch/match (shaded by quality score): ATCG/ATCG < 3 ≤ ATCG/ATCG < 22 ≤ ATCG/ATCG < 33 ≤ ATCG/ATCG < 37 ≤ ATCG/ATCG < 40 ≤ ATCG/ATCG
Unaligned base: atcg    Masked matching base: atcg    Alignment gap: ‑    Deleted base: ‑