Predicted mutation
evidence	seq id	position	mutation	annotation	gene	description
RA	NC_000913	4,061,961	Δ1 bp	coding (1386/1458 nt)	b3876 ←	putative permease

Read alignment evidence...
	seq id	position		ref	new	freq	score (cons/poly)	reads	annotation	genes	product
*	NC_000913	4,061,959	0	C	.	93.2%	227.9 / 8.1	60	coding (1388/1458 nt)	b3876	putative permease
Reads supporting (aligned to +/- strand):  ref base C (4/0);  new base . (30/25);  total (35/25)
Fisher's exact test for biased strand distribution p-value = 1.30e-01
Kolmogorov-Smirnov test that lower quality scores support variant p-value = 1.00e+00

TTTTTTAAACGTAGGGAGGCCGCCACCCACCAGGATGGAAATAGCGGCTATTGACATTTATAACGTTACGGAAGCCCGTTTTTTCTTCTG‑TCGCCATCTCTTTATTTTTGCGTTGGTTGATTTCCTCAATAATCAATGCAAACCGT  >  NC_000913/4061885‑4062030                                                                           |                                                                         atttttACACGTAGGGAGGCCGTCACCGCCCAGGATGGAAAGAGCGGCTATTTACATTTATAACTTTACGGAAGcc                                                                         <  2:630996/75‑1 (MQ=255)   ttttAAACGTAGGGAGGCCGCCACCCACCAGGATGGAAATAGCGGCTATTGACATTTATAACGTTACGGAAGccgt                                                                       <  1:106431/76‑3 (MQ=255)   ttttAAACGTAGGGAGGCCGCCACCCACCAGGATGGAAATAGCGGCTATTGACATTTATAACGTTACGGAAGccgt                                                                       >  2:2223860/1‑74 (MQ=255)   ttttAAACGTAGGGAGGCCGCCACCCACCAGGATGGAAATAGCGGCTATTGACATTTATAACGTTACGGAAGccgt                                                                       >  2:2215476/1‑74 (MQ=255)    tttAAACGTAGGGAGGCCGCCACCCACCAGGATGGAAATAGCGGCTATTGACATTTATAACGTTACGGAAGccgtt                                                                      <  1:2095782/76‑4 (MQ=255)      tAAACGTAGGGAGGCCGCCACCCACCAGGATGGAAATAGCGGCTATTTACATTTATAACGTTGCGGACG‑CCGtttt                                                                   >  2:4858227/1‑76 (MQ=255)       aaaCGTAGGGAGGCCGCCACCCACCAGGATGGAAATAGCGGCTATTGACATTTATAACGTTACGGAAG‑CCGttttt                                                                  <  2:3802171/76‑1 (MQ=255)        aaCGTAGGGAGGCCGCCACCCACCAGGATGGAAATAGCGGCTATTTACATTTTTGACGTTTCGGAAG‑GCGtttttt                                                                 >  2:2967776/1‑76 (MQ=255)        aaCGTAGGGAGGCCGCCACCCACCAGGATGGAAATAGCGGCTATTGACATTTATAACGTTACGGAAGCCGGttttt                                                                  >  2:3481918/1‑76 (MQ=255)         aCGTAGGGAGGCCGCCACCCCCCAGGATGGAAATAGCGGCTAATGAAATTTATACATTTACGGAAGCCGTtttttt                                                                 >  2:4033610/1‑76 (MQ=255)         aCGTAGGGAGGCCGCCACCCACCAGGATGGAAATAGCGGCTATTGACATTTATAACGTTACGGAAGCCGGtttttt                                                                 >  2:4003102/1‑76 (MQ=255)         aCGTAGGGAGGCCGCCACCCACCAGGATGGAAATAGCGGCTATTGACATTTATAACGTTACGGAAGCCGGtttttt                                                                 >  2:1286497/1‑76 (MQ=255)          cGTAGGGAGGCCGCCACCCACCAGGATGGAAATAGCGGCTATTGACATTTATAACGTTACGGAAG‑CCGTTTTttct                                                               <  1:3558428/76‑1 (MQ=255)           gTAGGGAGGCCGCCACCCACCAGGATGGAAATAGCGGCTATTTACATTTATAACGGTACGGAAGGCGGtttttttt                                                               >  2:1294737/1‑74 (MQ=255)           gTAGGGAGGCCGCCACCCACCAGGATGGAAATAGCGGCTATTGACATTTATAACGTTACGGAAG‑CCGTTTTttctt                                                              <  2:2445198/76‑1 (MQ=255)           gTAGGGAGGCCGCCACCCACCAGGATGGAAATAGCGGCTATTGACATTTATAACGTTACGGAAG‑CCGTTTTttctt                                                              >  1:1910202/1‑76 (MQ=255)             aGGGAGGCCGCCACCCACCAGGATGGAAATAGCGGCTATTGACATTTATAACGTTACGGAAG‑CCGTTTTTtcttct                                                            <  1:2825997/76‑1 (MQ=255)             aGGGAGGCCGCCACCCACCAGGATGGAAATAGCGGCTATTGACATTTATAACGTTACGGAAG‑CCGTTTTTtcttct                                                            >  1:1906598/1‑76 (MQ=255)             aGGGAGGCCGCCACCCACCAGGATGGAAATAGCGGCTATTGACATTTATAACGTTACGGAAG‑CCGGTTTTtcttct                                                            >  1:4246383/1‑76 (MQ=255)               ggAGGCCGCCACCCACCAGGATGGAAATAGCGGCTATTGACATTTATTATGTTACGGGAG‑GCGGTTTTTCTTCTG‑t                                                         >  1:731516/1‑76 (MQ=255)                gAGGCCGCCACCCACCAGGATGGAAATAGCGGCTATTGACATTTATAACGTTACGTAAG‑CCGTTTTTTCTTCTG‑Tc                                                        <  2:1544768/76‑1 (MQ=255)                gAGGCCGCCACCCACCAGGATGGAAATAGCGGCTATTGACATTTATAACGGTACGGAAG‑CCGGTTTTTCTTCTG‑Tc                                                        >  1:928307/1‑76 (MQ=255)                     cgccACCCACCAGGATGGAAATAGCGGCTATTGACATTTATAACGTTACGGAAG‑CCGTTTTTTCTTCTG‑TCGCCAt                                                   <  1:354916/76‑1 (MQ=255)                      gccACCCACCAGGATGGAAATAGCGGCTATTGACATTTATAACGTTACGGAAG‑CCGTTTTTTTTTCTT‑TCGCCAtt                                                  >  1:4443433/1‑75 (MQ=255)                       ccgcccgccAGGATGGAAATAGCGGCTATTGACATTTAGAACGTTACGGAAG‑CCGTTTTTTCTTCTG‑TCGCCAtct                                                 <  2:4493815/73‑1 (MQ=255)                       ccacccacCAGGATGGAAATAGCGGCTATTGACATTTATAACGTTACGGAAG‑CCGTTTTTTCTTCTG‑TCGCCAtct                                                 <  2:3154280/76‑1 (MQ=255)                        caccccccAGGCTTGAAATAGCGGATATTGACATTTATAACGTTTGGGTTG‑CCGTTTTTTCTTCTG‑TCGCCTtctc                                                <  2:1087651/76‑1 (MQ=255)                        cacccaccAGGATGGAAATAGCGGCTATTGACATTTATAACGTTACGGAAG‑GCGTTTGTTTTTCTT‑TTGCCCtctc                                                >  2:1306218/1‑76 (MQ=255)                         aaccaccaGGATGGAAATAGCGGCTAATGACATTTCTAAAGTTACGGCAG‑CCGTGTTTTTTTTTG‑TCGCCctctct                                               >  1:4698683/3‑76 (MQ=255)                          cccaccAGGATGGAAATAGCGGCTATTGACATTTATAACGTTACGGAAG‑CCGTTTTTTTTTCTG‑TCGCCCTCTCtt                                              >  2:4208908/1‑76 (MQ=255)                            caccaGGATGGAAATAGCGGCTATTGACATTTATAACGTTACGGAAGCCGGTTTTTT‑TTCTGTTCGCC‑TCTCtttt                                            >  1:2898174/1‑75 (MQ=255)                               caGGATGGAAATAGCGGCTATTGACATTTATAACGTTACGGGAG‑CCGTTTTTTCTTCTG‑TCGCCATCTCTTTAttt                                         <  1:885465/76‑1 (MQ=255)                                 ggATGGAAATAGCGGCTATTGACATTTATAACGTTACGGAAG‑CCGTTTTTTCTTCTG‑TCGCCATCTCTTTAttttt                                       <  1:1288376/76‑1 (MQ=255)                                  gATGGAAATAGCGGCTATTGACATTTATAACGTTACGGAAG‑CCGTTTTTTTTTCTG‑TCGCCCTCTCTttttttttt                                      >  1:100121/1‑75 (MQ=255)                                  gATGGAAATAGCGGCTATTGACATTTATAACGTTACGGAAG‑CCGTTTTTTCTTCTG‑TCGCCATCTCTTTATTTTTg                                      <  2:1419655/76‑1 (MQ=255)                                    tGGAAATAGCGGCTATTGACATTTATAACGTTACGGAAG‑CCGGTTTTTCTTCTG‑TCGCCATCTCTTTATTTTTTCg                                    >  1:4405425/1‑76 (MQ=255)                                     ggAACTAGCGGCTATTGACATTTATAACGTTACGGACG‑CCGTTTTTTCTTCTG‑TCGCCATCTCTTTATTTTTGCgt                                   <  1:1252061/76‑1 (MQ=255)                                     ggAAATAGCGGCTATTGAGATTTATAACGTTACGGAAG‑CCGTTTTTTCTTCTG‑TCGCCATCTCTTTATTTTTGCgt                                   <  2:543317/76‑1 (MQ=255)                                     ggAAATAGCGGCTATTGACATTTATAACGTTACGGAAG‑CCGTTTTTTCTTCTG‑TCGCCATCTCTTTATTTTTGCgt                                   >  2:1030387/1‑76 (MQ=255)                                     ggAAATAGCGGCTATTGACATTTATAACGTTACGGAAG‑CCGTTTTTTCTTCTG‑TCGCCATCTCTTTATTTTTGCgt                                   <  2:496082/76‑1 (MQ=255)                                       aaaTAGCGGCTATTGACATTTATAACGTTACGGAAG‑CCGTTTTTTCTTCTG‑TCGCCATCTCTTTATTTTTGCgttg                                 <  2:3382741/76‑1 (MQ=255)                                          tAGCGGCTATTGACATTTATAACGTTACGGAAG‑CCGTTTTTTCTTCTG‑TCGCCCTCTCTTTATTTTTGCgttggtt                              >  1:1039484/1‑76 (MQ=255)                                          tAGCGGCTATTGACATTTATAACGTTACGGAAG‑CCGTTTTTTCTTCTG‑TCGCCATCTCTTTATTTTTGCgttggtt                              <  2:623585/76‑1 (MQ=255)                                           aGCGGCTATTGACATTTATAACGTTACGGGAG‑CCGTTTTTTTTTCTT‑TCGCCCTCTCTTTTTTTTTTCgttggttt                             >  2:233179/1‑75 (MQ=255)                                           aGCGGCTATTGACATTTATAACGTTACGGAAG‑CCGTTTTTTCTTCTG‑TCGCCATCTCTTTATTTTTTCgttggttg                             >  2:4354252/1‑76 (MQ=255)                                            gCGGCTATTGACATTTATAACGTTACGGAAG‑CCGTTTTTTCTTCTG‑TCGCCATCTCTTTATTTTTGCGTTGGTTGa                            <  2:541143/76‑1 (MQ=255)                                            gCGGCTATTGACATTTATAACGTTACGGAAG‑CCGTTTTTTCTTCCG‑TGCCCACCTCTTTATTTTTTGgttggttgt                            >  2:3439838/1‑75 (MQ=255)                                                cTATTGACATTTATAACGTTACGGAAG‑CCGTTTTTTCTTCTG‑TCGCCATCTCTTTATTTTTGCGTTGGTTGATTTc                        <  2:2898174/76‑1 (MQ=255)                                                 tATTGACATTTATAACGTTACGGAAG‑CCGTTTTTTCTTCTG‑TCGCCATCTCTTTATTTTTGCGTTGGTTGATTTcc                       >  2:4286116/1‑76 (MQ=255)                                                   ttGACATTTATAACGTTACGGAAG‑CCGTTTTTTCTTCTG‑TCGCCATCTCTTTATTTTTGCGTTGGTTGATTTCCTc                     >  1:4760127/1‑76 (MQ=255)                                                     gACATTTATAACGTTACGGAAG‑CCGGTTTTTCTTCTG‑TCGCCATCTCTTTATTTTTGCGTTGGTTGATTTCCTCaa                   >  2:903506/1‑76 (MQ=255)                                                        aTTTATAACGTTACGGAAG‑CCGTTTTTTCTTCTG‑TCGCCATCTCTTTATTTTTGCGTTGGTTGATTTCCTCaataa                >  2:1132534/1‑76 (MQ=255)                                                         tttATAACGTTACGGAAG‑CCGTTTTTTCTTCTG‑TCGCCATCTCTTTATTTTTGCGTTGGTTGATTTCCTCaataat               >  2:1606461/1‑76 (MQ=255)                                                              aaCGTTACGGAAG‑CCGTTTTTTCTTCTG‑TCGCCATCTCTTTATTTTTGCGTTGGTTGATTTCCTCAATAATCAATg          <  2:1946355/76‑1 (MQ=255)                                                               aCGTTACGGAAG‑CCGTTTTTTCTTCTG‑TCGCCATCTCTTTATTTTTGCGTTGGTTGATTTCCTCAATAATCAATGc         <  1:3249684/76‑1 (MQ=255)                                                                cGTTACGGAAG‑CCGTTTTTTCTTCTG‑TCGCCATCTCTTTATTTTTGCGTTGGTTGATTTCCTCAATAATCAATGCa        >  2:4117178/1‑76 (MQ=255)                                                                 gTTACGGAAG‑CCGTTTTTTCTTCTG‑TCGCCATCTCTTTATTTTTGCGTTGGTTGATTTCCTCAATAATCAATGCaa       >  1:780116/1‑76 (MQ=255)                                                                 gTTACGGAAG‑CCGTTTTTTCTTCTG‑TCGCCATCTCTTTATTTTTGCGTTGGTTGATTTCCTCAATAATCAATGCaa       >  1:4383586/1‑76 (MQ=255)                                                                 gTTACGGAAG‑CCGTTTTTTCTTCTG‑TCGCCATCTCTTTATTTTTGCGTTGGTTGATTTCCTCAATAATCAATGCaa       >  1:2868687/1‑76 (MQ=255)                                                                 gTTACGGAAG‑CCGTTTTTTCTTCTG‑TCGCCATCTCTTTATTTTTGCGTTGGTTGATTTCCTCAATAATAAATGCaa       >  1:4428885/1‑76 (MQ=255)                                                                  ttACGGAAG‑CCGTTTTTTCTTCTG‑TCGCCATCTCTTTATTTTTGCGTTGGTTGATTTCCTCAATAATCAATGCaaa      >  1:596010/1‑76 (MQ=255)                                                                  ttACGGAAG‑CCGTTTTTTCTTCTG‑TCGCCATCTCTTTATTTTTGCGTTGGTTGATTTCCTCAATAATCAATGCaaa      <  1:4354252/76‑1 (MQ=255)                                                                  ttACGGAAG‑CCGTTTTTTCTTCTG‑TCGCCATCTCTTTATTTTTGCGTTGGTTGATTTCCTCAATAATCAATGCaaa      <  2:780116/76‑1 (MQ=255)                                                                     cGGAAG‑CCGTTTTTTCTTCTG‑TCGCCATCTCTTTATTTTTGCGTTGGTTGATTTCCTCAATAATCAATGCAAACCg   <  2:508721/76‑1 (MQ=255)                                                                      ggAAG‑CCGTTTTTTCTTCTG‑TCGCCATCTCTTTATTTTTGCGTTGGTTGATTTCCTCAATAATCAATGCAAACCGt  <  1:3026310/76‑1 (MQ=255)                                                                      ggAAG‑CCGTTTTTTCTTCTG‑TCGCCATCTCTTTATTTTTGCGTTGGTTGATTTCCTCAATAATCAATGCAAACCGt  >  2:799044/1‑76 (MQ=255)                                                                           |                                                                         TTTTTTAAACGTAGGGAGGCCGCCACCCACCAGGATGGAAATAGCGGCTATTGACATTTATAACGTTACGGAAGCCCGTTTTTTCTTCTG‑TCGCCATCTCTTTATTTTTGCGTTGGTTGATTTCCTCAATAATCAATGCAAACCGT  >  NC_000913/4061885‑4062030

Alignment Legend
Aligned base mismatch/match (shaded by quality score): ATCG/ATCG < 3 ≤ ATCG/ATCG < 7 ≤ ATCG/ATCG < 20 ≤ ATCG/ATCG < 40 ≤ ATCG/ATCG
Unaligned base: atcg    Masked matching base: atcg    Alignment gap: ‑    Deleted base: ‑