Predicted mutation
evidence	seq id	position	mutation	freq	annotation	gene	description
RA	NC_002947	5,338,677	T→C	11.4%	noncoding (353/395 nt)	PP_mr53 →	CrcZ ncRNA

Read alignment evidence...
	seq id	position		ref	new	freq	score (cons/poly)	reads	annotation	genes	product
*	NC_002947	5,338,677	0	T	C	11.4%	110.6 / 5.7	44	noncoding (353/395 nt)	PP_mr53	CrcZ ncRNA
Reads supporting (aligned to +/- strand):  ref base T (18/21);  new base C (3/2);  total (21/23)
Fisher's exact test for biased strand distribution p-value = 6.58e-01
Kolmogorov-Smirnov test that lower quality scores support variant p-value = 4.32e-01

ATCAGCGGCCAAAGCAATCCGTTTGCTCTTTACCCCCGGTTTGGGGGTCGTCCACAAGCTTCGAGATTTGTGGACAGGGCACTCAACAAAAACAAGAAGCCCAGCAAAAAAACAATAAGAGCACGCAACGACTTCTTGGGGAGCTTAGGCTCCCCTTGTCGTTTCTACCCTTCTGGCAGGCATCCTGCTACCCGCCTACACCATTCCCCGAGTAAATGCTAGAATCCCCGCCCATCATGCGGCCATTCTCCTATTCTTGGCCGAACATTCCTTCACACAGTGCATCCCATGCTG  >  NC_002947/5338533‑5338826                                                                                                                                                 |                                                                                                                                                      aTCAGCGGCCAAAGCAATCCGTTTGCTCTTTACCCCCGGTTTGGGGGTCGTCCACAAGCTTCGAGATTTGTGGACAGGGCACTCAACAAAAACAAGAAGCCCAGCAAAAAAACAATAAGAGCACGCAACGACTTCTTGGGGAGCTTa                                                                                                                                                     >  1:769777/1‑147 (MQ=255) aTCAGCGGCCAAAGCAATCCGTTTGCTCTTTACCCCCGGTTTGGGGGTCGTCCACAAGCTTCGAGATTTGTGGACAGGGCACTCAACAAAAACAAGAAGCCCAGCAAAAAAACAATAAGAGCACGCAACGACTTCTTGGGGAGCTTa                                                                                                                                                     <  2:769777/147‑1 (MQ=255)    aGCGGCCAAAGCAATCCGTTTGCTCTTTACCCCCGGTTTGGGGGTCGTCCACAAGCTTCGAGATTTGTGGACAGGGCACTCAACAAAAACAAGAAGCCCAGCAAAAAAACAATAAGAGCACGCAACGACTTCTTGGGGAGCTTAGGCTcc                                                                                                                                               >  2:293268/1‑150 (MQ=255)     gCGGCCAAAGCAATCCGTTTGCTCTTTACCCCCGGTTTGGGGGTCGTCCACAAGCTTCGAGATTTGTGGACAGGGCACTCAACAAAAACAAGAAGCCCAGCAAAAAAACAATAAGAGCACGCAACGACTTCTTGGGGAGCTTAGGCTccc                                                                                                                                              >  2:19958/1‑150 (MQ=255)       ggCCAAAGCAATCCGTTTGCTCTTTACCCCCGGTTTGGGGGTCGTCCACAAGCTTCGAGATTTGTGGACAGGGCACTCAACAAAAACAAGAAGCCCAGCAAAAAAACAATAAGAGCACGCAACGACTTCTTGGGGAGCTTAGGCTCCCCt                                                                                                                                            <  2:504805/150‑1 (MQ=255)                           tctTTACCCCCGGTTTGGGGGTCATCCACAAGCTTCGAGATTTGTGGACAGGGCACTCAACAAAAACAAGAAGCCCAGCAAAAAAACAATAAGAGCACGCAACGACTTCTTGGGGAGCTTAGGCTCCCCTTGTCGTTTCTACCCTTCTgg                                                                                                                        >  2:711784/1‑150 (MQ=255)                           tctTTACCCCAGGTTTGGGGGTCGTCCACAAGCTTCGAGATTTGTGGACAGGGCACTCAACAAAAACAAAAAGAAAAAAAAAAAAACAATAAGAGCACGCAACGACTTCTTGGGGAGCTTAGGCTCCCCTTGTCGTTTCTACCCTTCTgg                                                                                                                        <  2:421118/150‑1 (MQ=255)                             tttACCCCCGGTTTGGGGGTCGTCCACAAGCTTCGAGATTTGTGGACAGGGCACTCAACAAAAACAAGAAGCCCAGCAAAAAAACAATAAGAGCACGCAACGACTTCTTGGGGAGCTTAGGCTCCCCTTGTCGTTTCTACCCTTCTggca                                                                                                                      <  1:19958/150‑1 (MQ=255)                             tttACCCCCGGTTTGGGGGTCGTCCACAAGCTTCGAGATTTGTGGACAGGGCACTCAACAAAAACAAGAAGCCCAGCAAAAAAACAATAAGAGCACGCAACGACTTCTTGGGGAGCTTAGGCTCCCCTTGTCGTTTCTACCCTTCTggca                                                                                                                      >  2:668441/1‑150 (MQ=255)                                 cccccGGTTTGGGGGTCGTCCACAAGCTTCGAGATTTGTGGACAGGGCACTCAACAAAAACAAGAAGCCCAGCAAAAAAACAATAAGAGCACGCAACGACTTCTTGGGGAGCTTAGGCTCCCCTTGTCGTTTCTACCCTTCTggcaggca                                                                                                                  >  2:46654/1‑150 (MQ=255)                                  ccccGGTTTGGGGGTCGTCCACAAGCTTCGAGATTTGTGGACAGGGCACTCAACAAAAACAAGAAGCCCAGCAAAAAAACAATAAGAGCACGCAACGACTTCTTGGGGAGCTTAGGCTCCCCTTGTCGTTTCTACCCTTCTGGCAGGCAt                                                                                                                 >  2:186473/1‑150 (MQ=255)                                        tttGGGGGTCGTCCACAAGCTTCGAGATTTGTGGACAGGGCACTCAACACGGAGAATAAGCCCAGCAAAAAAACAATAAGAGCACGCAACGACTTCTTGGGGAGCTTAGGCTCCCCTTGTCGTTTCTACCCTTCTGGCAGGCATCCTGCt                                                                                                           >  1:700825/1‑150 (MQ=255)                                              ggTCGTCCACAAGCTTCGAGATTTGTGGACAGGGCACTCAACAAAAACAAGAAGCCCAGCAAAAAAACAATAAGAGCACGCAACGACTTCTTGGGGAGCTTAGGCTCCCCTTGTCGtt                                                                                                                                     <  1:173341/118‑1 (MQ=255)                                              ggTCGTCCACAAGCTTCGAGATTTGTGGACAGGGCACTCAACAAAAACAAGAAGCCCAGCAAAAAAACAATAAGAGCACGCAACGACTTCTTGGGGAGCTTAGGCTCCCCTTGTCGtt                                                                                                                                     >  2:173341/1‑118 (MQ=255)                                              ggTCGTCCACAAGCTTCGAGATTTGTGGACAGGGCACTCAACAAAAACAAGAAGCCCAGCAAAAAAACAATAAGAGCACGCAACGACTTCTTGGGGAGCTTAGGCTCCCCTTGTCGTTTCTACCCTTCTGGCAGGCATCCTGCTACCCGc                                                                                                     >  2:341988/1‑150 (MQ=255)                                                   tcCACAAGCTTCGAGATTTGTGGACAGGGCACTCAACAAAAACAAGAAGCCCAGCAAAAAAACAATAAGAGCACGCAACGACTTCTTGGGGAGCTTAGGCTCCCCTTGTCGTTTCTACCCTTCTGGCAGGCATCCTGCTACCCGCCTaca                                                                                                <  1:46654/150‑1 (MQ=255)                                                      acaAGCTTCGAGATTTGTGGACAGGGCACTCAACAAAAACAAGAAGCCCAGCAAAAAAACAATAAGAGCACGCAACGACTTCTTGGGGAGCTTAGGCTCCCCTTGTc                                                                                                                                        <  1:16716/107‑1 (MQ=255)                                                      acaAGCTTCGAGATTTGTGGACAGGGCACTCAACAAAAACAAGAAGCCCAGCAAAAAAACAATAAGAGCACGCAACGACTTCTTGGGGAGCTTAGGCTCCCCTTGTc                                                                                                                                        >  2:16716/1‑107 (MQ=255)                                                         aGCTTCGAGATTTGTGGACAGGGCACTCAACAAAAACAAGAAGCCCAGCAAAAAAACAATAAGAGCACGCAACGACTTCTTGGGGAGCTTAGGCTCCCCTTGTCGTTTCTACCCTTCTGGCAGGCATCCTGCTACCCGCCTACACCATTc                                                                                          <  1:711784/150‑1 (MQ=255)                                                           cTTCGAGATTTGTGGACAGGGCACTCAACAAAAACAAGAAGCCCAGCAAAAAAACAATAAGAGCACGCAACGACTTCTTGGGGAGCTTAGGCTCCCCTTGTCGTTTCTACCCTTCTGGCAGGCATCCTGCTACCCGCCTACACCATTccc                                                                                        <  1:10846/150‑1 (MQ=255)                                                            ttCGAGATTTGTGGACAGGGCACTCAACAAAAACAAGAAGCCCAGCAAAAAAACAATAAGAGCACGCAACGACTTCTTGGGGAGCTTAGGCTCCCCTTGTCGTTTCTACCCTTCTGGCAGGCATCCTGCTACCCGCCTACACCATTcccc                                                                                       <  1:341988/150‑1 (MQ=255)                                                            ttCGAGATTTGTGGACAGAGCACTCAACAAAAACAAGAAGCCCAGCAAAAAAACAATAAGAGCACGCAACGACTTCTTGGAGAGCTTACGCTCCCCTTGTCGTTTCTACCCTTCTGGCAGGCATCCTGCTACCCGCCTACACCATTcccc                                                                                       <  1:796311/150‑1 (MQ=255)                                                              cGAGATTTGTGGACAGGGCACTCAACAAAAACAAGAAGCCCAGCAAAAAAACAATAAGAGCACGCAACGACTTCTTGGGGAGCTTAGGCTCCCCTTGTCGTTTCTACCCTTCTGGCAGGCATCCTGCTACCCGCCTACACCATTCCCCGa                                                                                     <  1:129165/150‑1 (MQ=255)                                                              cGAGATTTGTGGACAGGGCACTCAACAAAAACAAGAAGCCCAGCAAAAAAACAATAAGAGCACGCAACGACTTCTTGGGGAGCTTAGGCTCCCCTTGTCGTTTCTACCCTTCTGGCAGGCATCCTGCTACCCGCCTACACCATTCCCCGa                                                                                     <  2:793193/150‑1 (MQ=255)                                                                   tttGTGGACAGGGCACTCAACAAAAACAAGAAGCCCAGCAAAAAAACAATAAGAGCACGCAACGACTTCTTGGGGAGCTTAGGCTCCCCTTGTCGTTTCTACCCTTCTGGCAGGCATCCTGCTACACGCCTACACCATTCCCCGAGTaaa                                                                                <  1:186473/150‑1 (MQ=255)                                                                         gACAGGGCACTCAACAAAAACAAGAAGCCCAGCAAAAAAACAATAAGAGCACGCAACGACTTCTTGGGGAGCTTAGGCTCCCCTTGTCGTTTCTACCCTTCTGGCAGGCATCCTGCTACCCGCCTACACCATTCCCCGAGTAAATGCTAg                                                                          >  1:99244/1‑150 (MQ=255)                                                                             gggCACTCAACAAAAACAAGAAGCCCAGCAAAAAAACAATAAGAGCACGCAACGACTTCTTGGGGAGCTTAGGCTCCCCTTGTCGTTTCTACCCTTCTGGCAGGCATCCTGCTACCCGCCTACACCATTCCCCGAGTAAATGCTAGAATc                                                                      >  1:34295/1‑150 (MQ=255)                                                                                           aaCAAGAAGCCCAGCAAAAAAACAATAAGAGCACGCAACGACTTCTTGGGGAGCTTAGGCTCCCCTTGTCGTTTCTACCCTTCTGGCAGGCATCCTGCTACCCGCCTACACCATTCCCCGAGTAAATGCTAGAATCCCCGCCCATCATGc                                                        >  1:110719/1‑150 (MQ=255)                                                                                             cAAGAAGCCCAGCAAAAAAACAATAAGAGCACGCAACGACTTCTTGGGGAGCTTAGGCTCCCCTTGTCGTTTCTACCCTTCTGGCAGGCATCCTGCTACCCGCCTACACCATTCCCCGAGTAAATGCTAGAATCCCCGCCCATCATGCgg                                                      <  2:99244/150‑1 (MQ=255)                                                                                                     ccAGCAAAAAAACAATAAGAGCACGCAACGACTTCTTGGGGAGCTTAGGCTCCCCTTGTCGTTTCTACCCTTCTGGCAGGCATCCTGCTACCCGCCTACACCAt                                                                                            <  1:525672/104‑1 (MQ=255)                                                                                                     ccAGCAAAAAAACAATAAGAGCACGCAACGACTTCTTGGGGAGCTTAGGCTCCCCTTGTCGTTTCTACCCTTCTGGCAGGCATCCTGCTACCCGCCTACACCAt                                                                                            >  2:525672/1‑104 (MQ=255)                                                                                                     ccAGCAAAAAAACAATAAGAGCACGCAACGACTTCTTGGGGAGCTTAGGCTCCCCTTGTCGTTTCTACCCTTCTGGCAGGCATCCTGCTACCCGCCTACACCATTCCCCGAGTAAATGCTAGAATCCCCGCCCATCATGCGGCCATtctc                                              <  2:110719/150‑1 (MQ=255)                                                                                                      aaGCAAAAAAACAATAAGAGCACGCAACGACTTCTTGGGGAGCTTAGGCTCCCCTTGTCGTTTCTACCCTTCTGGCAGGCATCCTGCTACCCGCCTACACCATTCCCCGAGTAAATGCTAGAATCCCCGCCCATCATGCGGCCATTCTcc                                             <  2:700825/149‑1 (MQ=255)                                                                                                             aaaaCAATAAGAGCACGCAACGACTTCTTGGGGAGCTTAGGCTCCCCTTGTCGTTTCTACCCTTCTGGCAGGCATCCTGCTACCCGCCTACACCATTCCCCGAGTAAATGCTAGAATCCCCGCCCATCATGCGGCCATTCTCCTATTCtt                                      <  1:698136/150‑1 (MQ=255)                                                                                                               aaCAATAAGAGCACGCAACGACTTCTTGGGGAGCTTAGGCTCCCCTTGTCGTTTCTACCCTTCTGGCAGGCATCCTGCTACCCGCCTACACCATTCCCCGAGTAAATGCTAGAATCCCCGCCCATCATGCGGCCATTCTCCTATTCTTgg                                    >  1:260325/1‑150 (MQ=255)                                                                                                                   aTAAGAGCACGCAACGACTTCTTGGGGAGCTTAGGCTCCCCTTGTCGTTTCTACCCTTCTGGCAGGCATCCTGCTACCCGCCTACACCATTCCCCGAGTAAATGCTAGAATCCCCGCCCATCATGCGGCCATTCTCCTATTCtt                                      >  2:497036/1‑144 (MQ=255)                                                                                                                   aTAAGAGCACGCAACGACTTCTTGGGGAGCTTAGGCTCCCCTTGTCGTTTCTACCCTTCTGGCAGGCATCCTGCTACCCGCCTACACCATTCCCCGAGTAAATGCTAGAATCCCCGCCCATCATGCGGCCATTCTCCTATTCtt                                      <  1:497036/144‑1 (MQ=255)                                                                                                                    tAAGAGCACGCAACGACTTCTTGGGGAGCTTAGGCTCCCCTTGTCGTTTCTACCCTTCTGGCAGGCATCCTGCTACCCGCCTACACCATTCCCCGAGTAAATGCTAGAATccc                                                                    <  1:32716/113‑1 (MQ=255)                                                                                                                    tAAGAGCACGCAACGACTTCTTGGGGAGCTTAGGCTCCCCTTGTCGTTTCTACCCTTCTGGCAGGCATCCTGCTACCCGCCTACACCATTCCCCGAGTAAATGCTAGAATccc                                                                    >  2:32716/1‑113 (MQ=255)                                                                                                                                   acgacaaggggAGCCTAAGCTCCCCTTGTCGTTTCTACCCTTCTGGCAGGCATCCTGCTACCCGCCTACACCATTCCCCGAGTAAATGCTAGAATCCCCGCCCATCATGCGGCCATTCTCCTATTCTTGGCCGAACATTCCTTc                      <  1:719269/137‑1 (MQ=255)                                                                                                                                   acgacaaggggAGCCTAAGCTCCCCTTGTCGTTTCTACCCTTCTGGCAGGCATCCTGCTACCCGCCTACACCATTCCCCGAGTAAATGCTAGAATCCCCGCCCATCATGCGGCCATTCTCCTATTCTTGGCCGAACATTCCTTc                      >  2:719269/8‑144 (MQ=255)                                                                                                                                     gacaaggggAGCCTAAGCTCCCCTTGTCGTTTCTACCCTTCTGGCAGGCATCCTGCTACCCGCCTACACCATTCCCCGAGTAAATGCTAGAATCCCCGCCCATCATGCGGCCATTCTCCTATTCTTGGCCGAACATTCCTTCACACAGTg              >  2:683381/6‑150 (MQ=255)                                                                                                                                          ggggAGCCTAAGCTCCCCTTGTCGTTTCTACCCTTCTGGCAGGCATCCTGCTACCCGCCTACACCATTCCCAGAGTAAATGCTAGAATCCCCGCCCATCATGCGGCCa                                                   <  1:792838/108‑1 (MQ=255)                                                                                                                                          ggggAGCCTAAGCTCCCCTTGTCGTTTCTACCCTTCTGGCAGGCATCCTGCTACCCGCCTACACCATTCCCAGAGTAAATGCTAGAATCCCCGCCCATCATGCGGCCa                                                   >  2:792838/1‑108 (MQ=255)                                                                                                                                                 ttAGGCTCCCCTTGTCGTTTCTACCCTTCTGGCAGGCATCCTGCTACCCGCCTACACCATTCCCCGAGTAAATGCTAGAATCCCCGCCCATCATGCGGCCATTCTCCTATTCTTGGCCGAACATTCCTTCACACAGTGCATCCCATGCTg  >  1:536459/1‑150 (MQ=255)                                                                                                                                                 |                                                                                                                                                      ATCAGCGGCCAAAGCAATCCGTTTGCTCTTTACCCCCGGTTTGGGGGTCGTCCACAAGCTTCGAGATTTGTGGACAGGGCACTCAACAAAAACAAGAAGCCCAGCAAAAAAACAATAAGAGCACGCAACGACTTCTTGGGGAGCTTAGGCTCCCCTTGTCGTTTCTACCCTTCTGGCAGGCATCCTGCTACCCGCCTACACCATTCCCCGAGTAAATGCTAGAATCCCCGCCCATCATGCGGCCATTCTCCTATTCTTGGCCGAACATTCCTTCACACAGTGCATCCCATGCTG  >  NC_002947/5338533‑5338826

Alignment Legend
Aligned base mismatch/match (shaded by quality score): ATCG/ATCG < 3 ≤ ATCG/ATCG < 12 ≤ ATCG/ATCG < 32 ≤ ATCG/ATCG < 41 ≤ ATCG/ATCG
Unaligned base: atcg    Masked matching base: atcg    Alignment gap: ‑    Deleted base: ‑