Read alignment evidence...
	seq id	position		ref	new	freq	score (cons/poly)	reads	annotation	genes	product
*	CP000730	1,797,772	0	G	C	30.0%	27.8 / 16.3	21	R7G (CGC→GGC)	phoR	sensor histidine kinase
Reads supporting (aligned to +/- strand):  ref base G (9/5);  new base C (5/1);  total (14/7)
Fisher's exact test for biased strand distribution p-value = 6.13e-01
Kolmogorov-Smirnov test that lower quality scores support variant p-value = 8.42e-01
Rejected as consensus: Frequency below/above cutoff threshold.

AAATATATGATCTTGCATCTGTTGCTAGAGCTTGTTCGTGTTTTTCTGATAAAACATATGTGATGGAAGCGTGAATAATAATGCCTAATGTAACAAAACTGATAATTAATATACTGCTTATCAATAACATTAAGCGGTGGTGAAACTTCATCATTGTTCTTTAGGTCTTTCCAATTTATAGCCTAAGCCACGCACAGTTTTAATAAGTTGTGGCTTCTTAGGATTATCTTCTAATTTATCTCTTAAATGACTGATATGTACATCAACAATTC  >  CP000730/1797637‑1797908                                                                                                                                        |                                                                                                                                         aaataTATGATCTTGCATCTGTTGCTAGAGCTTGTTCGTGTTTTTCTGATAAAACATATGTGATGGAAGCGTGAATAATAATGCCTAATGTAACAAAACTGATAATTAATATACTGCTTATCAATAACATTAAGCggtggt                                                                                                                                     <  2:113811/141‑1 (MQ=255)         gATCTTGCATCTGTTGCTAGAGCTTGTTCGTGTTTTTCTGATAAAACATTTGTGATGAAAGCGTGAATAATAATGCCTAATGTAACAAAACTGATAATTAATATACTGCTTATCAATAACATTAAGCGGTGGTGAAACTtc                                                                                                                             <  1:226037/141‑1 (MQ=255)              tGCATCTGTTGCTAGAGCTTGTTCGTGTTTTTCTGATAAAACATATGTGATGGAAGCGTGAATAATAATGCCTAATGTAACAAAACTGATAATTAATATACTGCTTATCAATAACATTAAGCGGTGGTGAAACTTcatcat                                                                                                                        <  1:173530/141‑1 (MQ=255)                                           tttCTGATAAAACATATGTGATGGAAGCGTGAATAATAATGCCTAATGTAACAAAACTGATAATTAATATACTGCTTATCAATAACATTAAGCGGTGGTGAAACTTCATCATTGTTCTTTAGGTCTTTCCAATTTATAGcc                                                                                           >  1:278557/1‑141 (MQ=255)                                                      aCATATGTGATGGAAGCGTGAATAATAATGCCTAATGTAACAAAACTGATAATTAATATACTGCTTATCAATAACATTAAGCCGTGGTGAAACTTCATCATTGTTCTTTAGGTCTTTCCAATTTATAGCCTAAGCCACGca                                                                                >  1:260181/1‑141 (MQ=255)                                                           tgtgATGGAAGCGTGAATAATAATGCCTAATGTAACAAAACTGATAATTAATATACTGCTTATCAATAACATTAAGCCGTGGTGAAACTTCATCATTGTTCTTTAGGTCTTTCCCATTTATAGCCTAAGCCACGCACAGtt                                                                           >  1:41734/1‑141 (MQ=255)                                                              gATGGAAGCGTGAATAATAATGCCTAATGTAACAAAACTGATAATTAATATACTGCTTATCAATAACATTAAGCCGTGGTGAAACTTCATCATTGTTCTTTAGGTCTTTCCAATTTATAGCCTAAGCCACGCACAGTTTta                                                                        >  1:161962/1‑141 (MQ=255)                                                              gATGGAAGCGTGAATAATAATGCCTAATGTAACAAAACTGATAATTAATATACTGCTTATCAATAACATTAAGCCGTGGTGAAACTTCATCATTGTTCTTTAGGTCTTTCCAATTTATAGCCTAAGCCACGCACAGTTTta                                                                        <  1:328985/141‑1 (MQ=255)                                                                    aGCGTGAATAATAATGCCTAATGTAACAAAACTGATAATTAATATACTGCTTATCAATAACATTAAGCGGTGGTGAAACTTCATCATTGTTCTTTAGGTCTTTCCAATTTATAGCCTAAGCCACGCACAGTTTTAATAAGt                                                                  >  2:232975/1‑141 (MQ=255)                                                                       gTGAATAATAATGCCTAATGTAACAAAACTGATAATTAATATACTGCTTATCAATAACATTAAGCGGTGTTGAAACTTCATCATTGTTCTTTAGGTCTTTCCAATTTATAGCCTAAGCCACGCACAGTTTTAATAAGTtgt                                                               <  1:33932/141‑1 (MQ=255)                                                                               taatGCCTAATGTAACAAAACTGATAATTAATATACTGCTTATCAATAACATTAAGCGGTGGTGAAACTTCATCATTGTTCTTTAGGTCTTTCCAATTTATAGCCTAAGCCACGCACAGTTTTAATAAGTTGTGGcttctt                                                       <  2:88382/141‑1 (MQ=255)                                                                               taatGCCTAATGTAACAAAACTGATAATTAATATACTGCTTATCAATAACATTAAGCCGTGGTGAAACTTCATCATTGTTCTTTAGGTCTTTCCAATTTATAGCCTAAGCCACGCACAGTTTTAATAAGTTGTGGcttctt                                                       >  1:240825/1‑141 (MQ=255)                                                                                   gCCTAATGTAACAAAACTGAGAATTAATATACTGCTTATCAATAACAGTAAGCGGTGGTGAAACTTCATCATTGTTCTTTAGTTCTTTCCAATTTATAGCCTAAGCCACGCACAGTATTAATAAGTTGTGGCTTCTTAGGa                                                   >  2:84245/1‑141 (MQ=255)                                                                                           tAACAAAACTGATAATTAATATACTGCTTATCAATAACATTAAGCCGTGGTGAAACTTCATCATTGTTCTTTAGGTCTTTCCAATTTATAGCCTAAGCCACGCACAGTTTTAATAAGTTGTGGCTTCTTAGGATTAtcttc                                           >  2:131107/1‑141 (MQ=255)                                                                                                       taattaatATACTGCTTATCAATAACATTAAGCGGTGGTGAAACTTCATCATTGTTCTTTAGGTCTTTCCAATTTATAGCCTAAGCCACGCACAGTTTTAATAAGTTGTGGCTTCTTAGGATTATCTTCTAATTTATctct                               >  2:168966/1‑141 (MQ=255)                                                                                                       taattaatATACTGATTATCACTCTCATTAAGCTGTGGTGAATCTTCATCCTTGTTCTTTAGGTCTTTCCAATTTATAGCCTAAGCCTCGCACAGTTTTAATAAGTTGTGGCTTCTTAGGATTATCTTCTAATTTATctct                               <  2:68315/141‑1 (MQ=255)                                                                                                                  cTGCTTATCAATAACATTAAGCGGTGGTGAAACTTCATCATTGTTCTTTAGGTCTTTCCAATTTATAGCCTAAGCCACGCACAGTTTTAATAAGTTGTGGCTTCTTAGGATTATCTTCTAATTTATCTCTTAAATGACTGa                    >  1:71684/1‑141 (MQ=255)                                                                                                                      ttATCAATAACATTAAGCGGTGGTGAAACTTCATCATTGTTCTTTAGGTCTTTCCAATTTATAGCCTAAGCCACGCACAGTTTTAATAAGTTGTGGCTTCTTAGGATTATCTTCTAATTTATCTCTTAAATGACTGATATg                >  2:311953/1‑141 (MQ=255)                                                                                                                            aTAACATTAAGCGGTGGTGAAACTTCATCATTGTTCTTTAGGTCTTTCCAATTTATAGCCTAAGCCACGCACAGTTTTAATAAGTTGTGGCTTCTTAGGATTATCTTCTAATTTATCTCTTAAATGACTGATATGTACATc          >  1:187286/1‑141 (MQ=255)                                                                                                                               aCATTAAGCGGTGGTGAAACTTCATCATTGTTCTTTAGGTCTTTCCAATTTATAGCCTAAGCCACGCACAGTTTTAATAAGTTGTGGCTTCTTAGGATTATCTTCTAATTTATCTCTTAAATGACTGATATGTACATcaac       <  2:178453/141‑1 (MQ=255)                                                                                                                                    aaGCGGTGGTGAAACTTCATCATTGTTCTTTAGGTCTTTCCAATTTATAGCCTAAGCCACGCACAGTTTTAATAAGTTGTGGCTTCTTAGGATTATCTTCTAATTTATCTCTTAAATGACTGATATGTACATCAACAATTc  >  1:409431/1‑141 (MQ=255)                                                                                                                                    aaGCGGTGGTGAAACTTCATCATTGTTCTTTAGGTCTTTCCAATTTATAGCCTAAGCCACGCACAGTTTTAATAAGTTGTGGCTTCTTAGGATTATCTTCTAATTTATCTCTTAAATGACTGATATGTACATCAACAATTc  >  1:195118/1‑141 (MQ=255)                                                                                                                                        |                                                                                                                                         AAATATATGATCTTGCATCTGTTGCTAGAGCTTGTTCGTGTTTTTCTGATAAAACATATGTGATGGAAGCGTGAATAATAATGCCTAATGTAACAAAACTGATAATTAATATACTGCTTATCAATAACATTAAGCGGTGGTGAAACTTCATCATTGTTCTTTAGGTCTTTCCAATTTATAGCCTAAGCCACGCACAGTTTTAATAAGTTGTGGCTTCTTAGGATTATCTTCTAATTTATCTCTTAAATGACTGATATGTACATCAACAATTC  >  CP000730/1797637‑1797908

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