Predicted mutation
evidence	seq id	position	mutation	freq	annotation	gene	description
RA	NC_000913	2,330,385	C→T	8.1%	pseudogene (4018/4605 nt)	yfaS ←	pseudogene, bacterial alpha2‑macroglobulin YfaS variant family; putative membrane protein

Read alignment evidence...
	seq id	position		ref	new	freq	score (cons/poly)	reads	annotation	genes	product
*	NC_000913	2,330,385	0	C	T	8.1%	148.6 / 2.0	49	pseudogene (4018/4605 nt)	yfaS	pseudogene, bacterial alpha2‑macroglobulin YfaS variant family; putative membrane protein
Reads supporting (aligned to +/- strand):  ref base C (21/24);  new base T (2/2);  total (23/26)
Fisher's exact test for biased strand distribution p-value = 1.00e+00
Kolmogorov-Smirnov test that lower quality scores support variant p-value = 9.21e-01

GGCGTTCAACGGTCACCGGAATGTTACTTTGTTGAGCCATTTTTGCCGGCTCACGTCAGCGGACCTGCACATTTTGCGGCGATAATTCGTCACCAAAAGAGAGAATGTCCGGCACGCCCTGACCAACCCAACGCCAGTCTTCGCCCCCTCCAGTTAACTTATGTTTAGCCCATGCGCCCGCAGGCGCAGGCAAAACAACTGGAGGCATTGTCGCCATATATTTCGCCAGCCAGTTCATGGCCAGCGCGCGCTCAATAGTGGATTGCTCAGC  >  NC_000913/2330244‑2330514                                                                                                                                              |                                                                                                                                  ggCGTTCAACGGTCACCGGAATGTTACTTTGTTGAGCCATTTTTGCCGGCTCACGTCAGCGGACCTGCACATTTTGCGGCGATAATTCGTCACCAAAAGAGAGAATGTCCGGCACGCCCTGACCAACCCAACGCCAGTCTTCGccccc                                                                                                                             >  3:246586/1‑148 (MQ=255)      tCAACGGTCACCGGAATGTTACTTTGTTGAGCCATTTTTGCCGGCTCACGTCAGCGGACCTGCACATTTTGCGGCGATAATTCGTCACCAAAAGAGAGAATGTCCGGCACGCCCTGACCCACCCAACGCCAGTCTTCGCCCCCTcctg                                                                                                                        >  4:47478/1‑146 (MQ=255)      tCAACGGTCACCGGAATGTTACTTTGTTGAGCCATTTTTGCCGGCTCACGTCAGCGGACCTGCACATTTTGCGGCGATAATTCGTCACCAAAAGAGAGAATGTCCGGCACGCCCTGACCAACCCAACGCCAGTCTTCGCCCCCTCCAg                                                                                                                        >  3:264788/1‑148 (MQ=255)       cAACGGTCACCGGAATGTTACTTTGTTGAGCCATTTTTGCCGGCTCACGTCAGCGGACATGCACATTTTGCGGCGATAATTCGTCACCAAAAGAGAGAATGTCCGGCACGCCCTGACCAACCCAACGCCAGTCTTCGCCCCCTCCAGt                                                                                                                       >  6:370562/1‑148 (MQ=255)        aaCGGTCACCGGAATGTTACTTTGTTGAGCCATTTTTGCCGGCTCACGTCAGCGGACCTGCACATTTTGCGGCGATAATTCGTCACCAAAAGAGAGAATGTCCGGCACGCCCTGACCAACCCAACGCCAGTCTTCGCCCCCTCCAGt                                                                                                                       <  4:353643/147‑1 (MQ=255)                 cGGAATGTTACTTTGTTGAGCCATTTTTGCCGGCTCACGTCAGCGGACCTGCACATTTTGCGGCGATAATTCGTCACCAAAAGAGAGAATGTCCGGCACGCCCTGACCAACCCAACGCCAGTCTTCGCCCCCTCCAGTTAACTTAt                                                                                                               <  4:37060/146‑1 (MQ=255)                 cGGAATGTTACTTTGTTGAGCCATTTTTGCCGGCTCACGTCAGCGGACCTGCACATTTTGCGGCGATAATTCGTCACCAAAAGAGAGAATGTCCGGCACGCCCTGACCAACCCAACGCCAGTCTTCGCCCCCTCCAGTTAACTTAt                                                                                                               >  3:37060/1‑146 (MQ=255)                  ggAATGTTACTTTGTTGAGCCATTTTTGCCGGCTCACGTCAGCGGACCTGCACATTTTGCGGCGATAATTCGTCACCAAAAGAGAGAATGTCCGGCACGCCCTGACCAACCCAACGCCAGTCTTCGCCCCCTCCAGTTAACTTATGtt                                                                                                            <  4:264788/148‑1 (MQ=255)                     aTGTTACTTTGTTGAGCCATTTTTGCCGGCTCACGTCAGCGGACCTGCACATTTTGCGGCGATAATTCGTCACCAAAAGAGAGAATGTCCGGCACGCCCTGACCAACCCAACGCCAGTCTTCGCCCCCTCCAGTTAACTTATGtt                                                                                                            >  7:343224/1‑145 (MQ=255)                     aTGTTACTTTGTTGAGCCATTTTTGCCGGCTCACGTCAGCGGACCTGCACATTTTGCGGCGATAATTCGTCACCAAAAGAGAGAATGTCCGGCACGCCCTGACCAACCCAACGCCAGTCTTCGCCCCCTCCAGTTAACTTATGtt                                                                                                            <  8:343224/145‑1 (MQ=255)                       gTTACTTTGTTGAGCCATTTTTGCCGGCTCACGTCAGCGGACCTGCACATTTTGCGGCGATAATTCGTCACCAAAAGAGAGAATGTCCGGCACGCCCTGACCAACCCAACGCCAGTCTTCGCCCCCTCCAGTTAACTTATGtt                                                                                                            >  6:352012/1‑143 (MQ=255)                       gTTACTTTGTTGAGCCATTTTTGCCGGCTCACGTCAGCGGACCTGCACATTTTGCGGCGATAATTCGTCACCAAAAGAGAGAATGTCCGGCACGCCCTGACCAACCCAACGCCAGTCTTCGCCCCCTCCAGTTAACTTATGtt                                                                                                            <  5:352012/143‑1 (MQ=255)                       gTTACTTTGTTGAGCCATTTTTGCCGGCTCACGTCAGCGGACCTGCACATTTTGCGGCGATAATTCGTCACCAAAAGAGAGAATGTCCGGCACGCCCTGACCAACCCAACGCCAGTCTTCGCCCCCTCCAGTTAACTTATGTTTAGcc                                                                                                       >  3:170739/1‑148 (MQ=255)                       gTTACTTTGTTGAGCCATTTTTGCCGGCTCACGTCAGCGGACCTGCACATTTTGCGGCGATAATTCGTCACCAAAAGAGAGAATGTCCGGCACGCCCTGACCAACCCAACGCCAGTCTTCGCCCCCTCCAGTTAACTTATGTTTAGcc                                                                                                       >  1:250067/1‑148 (MQ=255)                       gTTACTTTGTTGAGCCATTTTTGCCGGCTCACGTCAGCGGACCTGCACATTTTGCGGCGATAATTCGTCACCAAAAGAGAGAATGTCCGGCACGCCCTGACCAACCCAACGCCAGTCTTCGCCCCCTCCAGTTAACTTATGTTTAGcc                                                                                                       >  4:292690/1‑148 (MQ=255)                        ttACTTTGTTGAGCCATTTTTGCCGGCTCACGTCAGCGGACCTGCACATTTTGCGGCGATAATTCGTCACCAAAAGAGAGAATGTCCGGCACGCCCTGACCAACCCAACGCCAGTCTTCGCCCCCTCCAGTTAACTTATGTTTAGccc                                                                                                      <  2:250067/148‑1 (MQ=255)                                  gAGCCATTTTTGCCGGCTCACGTCAGCGGCCCTGCACATTTTGCGGCGATAATTCGTCACCAAAAGAGAGAATGTCCGGCACGCCCTGACCAACCCAACGCCAGTCTTCGCCCCCTCCAGTTACCTTATGTTTAGCCCATGCGCCcg                                                                                             >  5:112585/1‑147 (MQ=255)                                         ttttGCCGGCTCACGTCAGCGGACCTGCACATTTTGCGGCGATAATTCGTCACCAAAAGAGAGAATGTCCGGCACGCCCTGACCAACCCAACGCCAGTCTTCGCCCCCTCCAGTTAACTTATGTTTAGCCCATGCGCCcgcaggcg                                                                                       >  8:290624/1‑146 (MQ=255)                                         ttttGCCGGCTCACGTCAGCGGACCTGCACATTTTGCGGCGATAATTCGTCACCAAAAGAGAGAATGTCCGGCACGCCCTGACCAACCCAACGCCAGTCTTCGCCCCCTCCAGTTAACTTATGTTTAGCCCATGCGCCcgcaggcg                                                                                       >  7:34351/1‑146 (MQ=255)                                         ttttGCCGGCTCACGTCAGCGGACCTGCACATTTTGCGGCGATAATTCGTCACCAAAAGAGAGAATGTCCGGCACGCCCTGACCAACCCAACGCCAGTCTTCGCCCCCTCCAGTTAACTTATGTTTAGCCCATGCGCCcgcaggcg                                                                                       >  5:364069/1‑146 (MQ=255)                                         ttttGCCGGCTCACGTCAGCGGACCTGCACATTTTGCGGCGATAATTCGTCACCAAAAGAGAGAATGTCCGGCACGCCCTGACCAACCCAACGCCAGTCTTCGCCCCCTCCAGTTAACTTATGTTTAGCCCATGCGCCcgcaggcg                                                                                       >  4:256082/1‑146 (MQ=255)                                          tttGCCGGCACACGTCAGCGGACCTGCACATTTTGCGGCGATAATTCGTCACCAAAAGAGACAATGTCCCGCACGCCCTGACCAACCCAAAGCCAGTCTTTGCCCCCTCCAGTTAACTTATCATTAGCACATGCGCCcgcaggcgcag                                                                                    >  7:312059/1‑148 (MQ=255)                                             gCCGGCTCACGTCAGCGGACCTGCACATTTTGCGGCGATAATTCGTCACCAAAAGAGAGAATGTCCGGCACGCCCTGACCAACCCAACGCCAGTCTTCGCCCCCACCAGTTAACTTATGTTTAGCCCATGCGCCCgcaggcgcaggc                                                                                  >  1:220956/1‑147 (MQ=255)                                               cGGCTCACGTCAGCGGACCTGCACATTTTGCGGCGATAATTCGTCACCAAAAGAGAGAATGTCCGGCACGCCCTGACCAACCCAACGCCAGTCTTCGCCCCCTCCAGTTAACTTATGTTTAGCCCATGCGCCCGCAGGCGCAGGCaaa                                                                               <  4:170739/148‑1 (MQ=255)                                                ggCTCACGTCAGCGGACCTGCACATTTTGCGGCGATAATTCGTCACCAAAAGAGAGAATGTCCGGCACGCCCTGACCAACCCAACGCCAGTCTTCGCCCCCTCCAGTTAACTTATGTTTAGCCCATGCGCCCGCAGGCGCAGGCaaaa                                                                              >  4:13927/1‑148 (MQ=255)                                                ggCTCACGTCAGCGGACCTGCACATTTTGCGGCGATAATTCGTCACCAAAAGAGAGAATGTCCGGCACGCCCTGACCAACCCAACGCCAGTCTTCGCCCCCTCCAGTTAACTTATGTTTAGCCCATGCGCCCGCAGGCGCAGGCaaaa                                                                              >  7:338934/1‑148 (MQ=255)                                                 gCTCACGTCAGCGGACCTGCACATTTTGCGGCGATAATTCGTCACCAACAGAGAGAATGTCCGGCACGCCCTGACCAACCCAACGCCAGTCTTCGCCCCCTCCAGTTAACTTATGTTTAGCCCATGCGCCCGCAGGCGCAGGCAAaac                                                                             <  1:234736/148‑1 (MQ=255)                                                  cTCACGTCAGCGGACCTGCACATTTTGCGGCGATAATTCGTCACCAAAAGAGAGAATGTCCGGCACGCCCTGACCAACCCAACGCCAGTCTTCGCCCCCTCCAGTTACCTTATGTTTAGCCCATGCGCCCGCAGGCGCAGGCAAaaca                                                                            <  3:292690/148‑1 (MQ=255)                                                  cTCACGTCAGCGGACCAGCACATTTTGCGGCGATAATTCGTCACCAAAAGAGACAATGTCCGGCACGCCCTGACCAACCCAACGCCAGTCATCGCCCCCTCCAGTTAACTTATGTTTAGCCCATGCGCCCGCAGGCGCAGGCAAaaca                                                                            <  3:47478/148‑1 (MQ=255)                                                  cTCACGGCAGCGGACCTGCACATTTTTCTGCGATAATTCGTCACCAAAAGAGAGAATGTCCGGCACGCCCTGACCAACCCAACGCCAGTCTTCGCCCCCTCCAGTTATCTTATGTTTAGCCCATGCGCCCGCAGGCGCAGGCAAaaca                                                                            <  6:346687/148‑1 (MQ=255)                                                     aCGTCAGCGGACCTGCACATTTTGCGGCGATAATTCGTCACCAAAAGAGAGAATGTCCGGCACGCCCTGACCAACCCAACGCCAGTCTTCGCCCCCTCCAGTTAACTTATGTTTAGCCCATGCGCCCGCAGGCGCAGGCAAaacaa                                                                           <  3:256082/146‑1 (MQ=255)                                                            cGGACCTGCACATTTTGCGGCGATAATTCGTCACCAAAAGAGAGAATGTCCGGCACGCCCTGACCAACCCAACGCCAGTCTTCGCCCCCTCCAGTTAACTTATGTTTAGCCCATGCGCCCGCAGGCGCAGGCAAAACAACTGGAGGCa                                                                  <  8:34351/148‑1 (MQ=255)                                                            cGGACCTGCACATTTTGCGGCGATAATTCGTCACCAAAAGAGAGAATGTCCGGCACGCCCTGACCAACCCAACGCCAGTCTTCGCCCCCTCCAGTTAACTTATGTTTAGCCCATGCGCCCGCAGGCGCAGGCAAAACAACTGGAGGCa                                                                  >  6:330164/1‑148 (MQ=255)                                                              gACCTGCACATTTTGCGGCGATAATTCGTCACCAAAAGAGAGAATGTCCGGCACGCCCTGACCAACCCAACGCCAGTCTTCGCCCCCTCCAGTTAACTTATGTTTAGCCCATGCGCCCGCAGGCGCAGGCAAAACAACTGGAGGCAtt                                                                <  7:133422/148‑1 (MQ=255)                                                                gcTGCACATTTTGCGGCGATAATTCGTCACCAAAAGAGAGAATGTCCGGCACGCCCTGACCAACCCAACGCCAGTCTTCGCCCCCTCCAGTTAACTTATGTTTAGCCCATGCGCCCGCAGGCGCAGGCAAAACAACTGGAGGCATTGt                                                              <  6:364069/147‑1 (MQ=255)                                                                 cTGCACATTTTGCGGCGATAATTCGTCACCAAAAGAGAGAATGTCCGGCACGCCCTGACCAACCCAACGCCAGTCTTCGCCCCCTCCAGTTAACTTATGTTTAGCCCATGCGCCCGCAGGCGCAGGCAAAACAACTGGAGGCATTGTc                                                             <  4:246586/148‑1 (MQ=255)                                                                   gCACATTTTGCGGCGATAATTCGTCACCAAAAGAGAGAATGTCCGGCACGCCCTGACCAACCCAACGCCAGTCTTCGCCCCCTCCAGTTAACTTATGTTTAGCCCATGCGCCCGCAGGCGCAGGCAAAACAACTGGAGGCATTGTCGc                                                           >  6:2900/1‑148 (MQ=255)                                                                        ttttGCGGCGATAATTCGTCACCAAAAGAGAGAATGTCCGGCACGCCCTGACCAACCCAACGCCAGTCTTCGCCCCCTCCAGTTAACTTATGTTTAGCCCATGCGCCCGCAGGCGCAGGCAAAACAACTGGAGGCATTGTCGCCatat                                                      <  7:290624/148‑1 (MQ=255)                                                                        ttttGCGGCGATAATTCGTCACCAAAAGAGAGAATGTCCGGCACGCCCTGACCAACCCAACGCCAGTCTTCGCCCCCTCCAGTTAACTTATGTTTAGCCCATGCGCCCGCAGGCGCAGGCAAAACAACTGGAGGCATTGTCGCCatat                                                      <  8:338934/148‑1 (MQ=255)                                                                        ttttGCGGCGATAATTCGTCACCAAAAGAGAGAATGTCCGGCACGCCCTGACCAACCCAACGCCAGTCTTCGCCCCCTCCAGTTAACTTATGTTTAGCCCATGCGCCCGCAGGCGCAGGCAAAACAACTGGAGGCATTGTCGCCatat                                                      <  5:370562/148‑1 (MQ=255)                                                                           tGCGGCGATAATTCGTCACCAAAAGAGAGAATGTCCGGCACGCCCTGACCAACCCAACGCCAGTCTTCGCCCCCTCCAGTTAACTTATGTTTAGCCCATGCGCCCGCAGGCGCAGGCAAAACAACTGGAGGCATTGTCGCCatatat                                                    <  5:2900/147‑1 (MQ=255)                                                                             cggcgATTATTCGTCTCCAAAAGAGATAATGTCCGGCACGCCCTGACCTACCCAACGCCAGTCTTTGCCCCCTCCATTTAACTTATGTTTAGCCCATGCGCCCGCAGGCGCAGGCAAAACAACTGGAGGCTTTGTCGCCATATATTTc                                                 <  8:312059/148‑1 (MQ=255)                                                                                                             ccGGCACGCCCTGACCAACCCAACGCCAGTCTTCGCCCCCTCCAGTTAACTTATGTTTAGCCCATGCGCCCGCAGGCGCAGGCAAAACAACTGGAGGCATTGTCGCCATATATTTCGCCAGCCAGTTCATGGCCAGCGCGCGCTCaa                  >  8:377393/1‑147 (MQ=255)                                                                                                              cGGCACGCCCTGACCAACCCAACGCCAGTCTTCGCCCCCTCCAGTTAACTTATGTTTAGCCCATGCGCCCGCAGGCGCAGGCAAAACAACTGGAGGCATTGTCGCCATATATTTCGCCAGCCAGTTCATGGCCAGCGCGCGCTCAAt                 <  7:377393/147‑1 (MQ=255)                                                                                                              cGGCACGCCCTGACCAACCCAACGCCAGTCTTCGCCCCCTCCAGTTAACTTATGTTTAGCCCATGCGCCCGCAGGCGCAGGCAAAACAACTGGAGGCATTGTCGCCATATATTTCGCCAGCCAGTTCATGGCCAGCGCGCGCTCAAt                 <  3:13927/147‑1 (MQ=255)                                                                                                                       cTGACCAACCCAACGCCAGTCTTCGCCCCCTCCAGTTAACTTATGTTTAGCCCATGCGCCCGCAGGCGCAGGCAAAACAACTGGAGGCATTGTCGCCATATATTTCGCCAGCCAGTTCATGGCCAGCGCGCGCTCAATAGTGGATTGc       <  5:330164/148‑1 (MQ=255)                                                                                                                            caacccaacGCCAGGCTTCGCCCCCTCCAGTTCACTTTTGTTTAGCCCCTGCGCCCGCAGGCGCAGGCAAAACAACTGGAGGCATTGGAGCCATATATGTCGCCAGCCAGTTCATGGCCAGCGCGCGCTCAATAGTGGATTGCTCAGc  <  6:112585/148‑1 (MQ=255)                                                                                                                                  aacGCCAGTCTTTGCCCCCTCCAGTTAACTTATGTTTAGCCCATGCGCCCGCAGGCGCAGGCAAaacaac                                                                          <  2:308952/70‑1 (MQ=255)                                                                                                                                  aacGCCAGTCTTTGCCCCCTCCAGTTAACTTATGTTTAGCCCATGCGCCCGCAGGCGCAGGCAAaacaac                                                                          >  1:308952/1‑70 (MQ=255)                                                                                                                                              |                                                                                                                                  GGCGTTCAACGGTCACCGGAATGTTACTTTGTTGAGCCATTTTTGCCGGCTCACGTCAGCGGACCTGCACATTTTGCGGCGATAATTCGTCACCAAAAGAGAGAATGTCCGGCACGCCCTGACCAACCCAACGCCAGTCTTCGCCCCCTCCAGTTAACTTATGTTTAGCCCATGCGCCCGCAGGCGCAGGCAAAACAACTGGAGGCATTGTCGCCATATATTTCGCCAGCCAGTTCATGGCCAGCGCGCGCTCAATAGTGGATTGCTCAGC  >  NC_000913/2330244‑2330514

Alignment Legend
Aligned base mismatch/match (shaded by quality score): ATCG/ATCG < 3 ≤ ATCG/ATCG < 14 ≤ ATCG/ATCG < 15 ≤ ATCG/ATCG < 32 ≤ ATCG/ATCG < 36 ≤ ATCG/ATCG
Unaligned base: atcg    Masked matching base: atcg    Alignment gap: ‑    Deleted base: ‑