Predicted mutation
evidence	seq id	position	mutation	annotation	gene	description
RA	REL606	1,290,472	Δ1 bp	coding (437/1014 nt)	hnr →	response regulator of RpoS

Read alignment evidence...
	seq id	position		ref	new	freq	score (cons/poly)	reads	annotation	genes	product
*	REL606	1,290,472	0	T	.	100.0%	274.6 / NA	56	coding (437/1014 nt)	hnr	response regulator of RpoS
Reads supporting (aligned to +/- strand):  ref base T (0/0);  new base . (37/19);  total (37/19)

TCTCTATCCCAGCATGTTTAATTCGCGCGTTGAGGAAGAGGAAAGGCTTTTTCGCGACTGGGATGCAATGGTTGATAACCCTGCCGCAGCGGCGAAATTATTACAGGAACTACAACCGCCGGTTCAGCAGGTGATTTCC  >  REL606/1290404‑1290542                                                                     |                                                                       tctcTATCCCAGCATGTTTAATTCGCGCGTTGAGGAAGAGGAAAGGCTTTTTCGCGACTGGGATGCAA‑GGTTGATa                                                                >  2:360352/1‑76 (MQ=255)  ctctATCCCAGCATGTTTAATTCGCGCGTTGAGGAAGAGGAAAGGCTTTTTCGCGACTGGGATGCAA‑GGTTGATaa                                                               >  2:1492827/1‑76 (MQ=255)      aTCCCAGCATGTTTAATTCGCGCGTTGAGGAAGAGGAAAGGCTTTTTCGCGACTGGGATGCAA‑GGTTGATAACCCt                                                           <  2:901917/76‑1 (MQ=255)      aTCCCAGCATGTTTAATTCGCGCGTTGAGGAAGAGGAAAGGCTTTTTCGCGACTGGGATGCAA‑GGTTGATAACCCt                                                           <  1:781422/76‑1 (MQ=255)      aTCCCAGCATGTTTAATTCGCGCGTTGAGGAAGAGGAAAGGCTTTTTCGCGACTGGGATGCAA‑GGTTGATAACCCt                                                           <  2:16797/76‑1 (MQ=255)       tCCCAGCATGTTTAATTCGCGCGTTGAGGAAGAGGAAAGGCTTTTTCGCGACTGGGATGCAA‑GGTTGATAACCCTg                                                          <  1:1448892/76‑1 (MQ=255)       tCCCAGCATGTTTAATTCGCGCGTTGAGGAAGAGGAAAGGCTTTTTCGCGACTGGGATGCAA‑GGTTGATAACCCTg                                                          >  2:733731/1‑76 (MQ=255)           aGCATGTTTAATTCGCGCGTTGAGGAAGAGGAAAGGCTTTTTCGCGACTGGGATGCAA‑GGTTGATAACCCTGCCGc                                                      <  2:911501/76‑1 (MQ=255)           aGCATGTTTAATTCGCGCGTTGAGGAAGAGGAAAGGCTTTTTCGCGACTGGGATGCAA‑GGTTGATAACCCTGCCGc                                                      <  2:1239391/76‑1 (MQ=255)              aTGTTTAATTCGCGCGTTGAGGAAGAGGAAAGGCTTTTTCGCGACTGGGATGCAA‑GGTTGATAACCCTGCCGCAgc                                                   >  1:372270/1‑76 (MQ=255)              aTGTTTAATTCGCGCGTTGAGGAAGAGGAAAGGCTTTTTCGCGACTGGGATGCAA‑GGTTGATAACCCTGCCGCAgc                                                   <  1:471427/76‑1 (MQ=255)              aTGTTTAATTCGCGCGTTGAGGAAGAGGAAAGGCTTTTTCGCGACTGGGATGCAA‑GGTTGATAACCCTGCCGCAgc                                                   >  1:187405/1‑76 (MQ=255)              aTGTTTAATTCGCGCGTTGAGGAAGAGGAAAGGCTTTTTCGCGACTGGGATGCAA‑GGTTGATAACCCTGCCGCAgc                                                   >  1:183221/1‑76 (MQ=255)                gTTTAATTCGCGCGTTGAGGAAGAGGAAAGGCTTTTTCGCGACTGGGATGCAA‑GGTTGATAACCCTGCCGCAgcgg                                                 >  1:59066/1‑76 (MQ=255)                 tttAATTCGCGCGTTGAGGAAGAGGAAAGGCTTTTTCGCGACTGGGATGCAA‑GGTTGATAACCCTGCCGCAgcggc                                                <  2:680138/76‑1 (MQ=255)                  ttAATTCGCGCGTTGAGGAAGAGGAAAGGCTTTTTCGCGACTGGGATGCAA‑GGTTGATAACCCTGCCGCAgcggcg                                               >  1:1491035/1‑76 (MQ=255)                    aaTTCGCGCGTTGAGGAAGAGGAAAGGCTTTTTCGCGACTGGGATGCAA‑GGTTGATAACCCTGCCGCAGCGGCGaa                                             <  2:1246946/76‑1 (MQ=255)                      ttCGCGCGTTGAGGAAGAGGANAGGCGTTTTCGCGACTAGGATGCAA‑GGTTGATAACCCTGCCGCAGCGGCGAAat                                           <  2:278757/76‑1 (MQ=255)                             gTTGAGGAAGAGGAAAGGCTTTTTCGCGACTGGGATGCAA‑GGTTGACAACCCTGCCGCAGCGGCGAAATTATTACa                                    <  1:1252120/76‑1 (MQ=255)                              ttGAGGAAGAGGAAAGGCTTTTTCGCGACTGGGATGCAA‑GGTTGATAACCCTGCCGCAGCGGCGAAATTATTACAg                                   >  1:607564/1‑76 (MQ=255)                                gaggaagaggaaAGGCTTTTTCGCGACTGGGATGCAA‑GGTTGATAACCCTGCCGCAGCGGCGAAATTATTACAGGa                                 >  1:983220/1‑76 (MQ=255)                                  ggaagaggaaAGGCTTTTTCGCGACTGGGATGCAA‑GGTTGATAACCCTGCCGCAGCGGCGAAATTATTACAGGAAc                               <  1:640262/76‑1 (MQ=255)                                   gaagaggaaAGGCTTTTTCGCGACTGGGATGCAA‑GGTTGATAACCCTGCCGCAGCGGCGAAATTATTACAGGAACt                              <  2:208067/76‑1 (MQ=255)                                   gaagaggaaAGGCTTTTTCGCGACTGGGATGCAA‑GGTTGATAACCCTGCCGCAGCGGCGAAATTATTACAGGAACt                              >  2:1054074/1‑76 (MQ=255)                                   gaagaggaaAGGCTTTTTCGCGACTGGGATGCAA‑GGTTGATAACCCTGCCGCAGCGGCGAAATTATTACAGGAACt                              <  1:47922/76‑1 (MQ=255)                                    aagaggaaAGGCTTTTTCGCGACTGGGATGCAA‑GGTTGATAACCCTGCCGCAGCGGCGAAATTATTACAGGAACTa                             <  2:1088910/76‑1 (MQ=255)                                    aagaggaaAGGCTTTTCCGCGTCTGGAATGCAA‑GGTTGATAACCCTGCCGCAGCGGCGAAATTATTACAGGAACTa                             <  2:118217/76‑1 (MQ=255)                                     agaggaaAGGCTTTTTCGCGACTGGGATGCAA‑GGTTGATAACCCTGCCGCAGCGGCGAAATTATTACAGGAACTAc                            >  1:583784/1‑76 (MQ=255)                                     agaggaaAGGCTTTTTCGCGACTGGGATGCAA‑GGTTGATAACCCTGCCGCAGCGGCGAAATTATTACAGGAACTAc                            >  2:1596476/1‑76 (MQ=255)                                     agaggaaAGGCTTTTTCGCGACTGGGATGCAA‑GGTTGATAACCCTGCCGCAGCGGCGAAATTATTACAGGAACTAc                            >  1:1442342/1‑76 (MQ=255)                                       gggaaAGGATTTTCCGCGACTGGGAGGC‑AGGGTTGATAACCCTGCCGCAGCGGCGAAATTATTACAGGAACTACaa                          <  1:1049263/75‑1 (MQ=255)                                       aggaaAGGCTTTTTCGCGACTGGGATGCAA‑GGTTGATAACCCTGCCGCAGCGGCGAAATTATTACAGGAACTACaa                          >  1:823517/1‑76 (MQ=255)                                       aggaaAGGCTTTTTCGCGACTGGGATGCAA‑GGTTGATAACCCTGCCGCAGCGGCGAAATTATTACAGGAACTACaa                          >  1:345243/1‑76 (MQ=255)                                        ggaaAGGCTTTTTCGCGACTGGGATGCAA‑GGTTGATAACCCTGCCGCAGCGGCGAAATTATTACAGGAACTACAAc                         >  1:733746/1‑76 (MQ=255)                                        ggaaAGGCTTTTTCGCGACTGGGATGCAA‑GGTTGATAACCCTGCCGCAGCGGCGAAATTATTACAGGAACTACAAc                         <  1:730487/76‑1 (MQ=255)                                         gaaAGGCTTTTTCGCGACTGGGATGCAA‑GGTTGATACCCCTGCCGCAGCGGCGAAATTATTACAGGAACTACAAcc                        <  2:1276767/76‑1 (MQ=255)                                         gaaAGGCTTTTTCGCGACTGGGATGCAA‑GGTTGATAACCCTGCCGCAGCGGCGAAATTATTACAGGAACTACAAcc                        <  2:1276748/76‑1 (MQ=255)                                           aaGGCTTTTTCGCGACTGGGATGCAA‑GGTTGATAACCCTGCCGCAGCGGCGAAATTATTACAGGAACTACAAccgc                      >  2:522497/1‑76 (MQ=255)                                           aaGGCTTTTTCGCGACTGGGATGCAA‑GGTTGATAACCCTGCCGCAGCGGCGAAATTATTACAGGAACTACAAccgc                      >  2:510578/1‑76 (MQ=255)                                           aaGGCTTTTTCGCGACTGGGATGCAA‑GGTTGATAACCCTGCCGCAGCGGCGAAATTATTACAGGAACTACAAccgc                      >  2:1318982/1‑76 (MQ=255)                                           aaGGCTTTTTCGCGACTGGGATGCAA‑GGTTGATAACCCTGCCGCAGCGGCGAAATTATTACAGGAACTACAAccgc                      >  2:1601118/1‑76 (MQ=255)                                           aaGGCTTTTTCGCGACTGGGATGCAA‑GGTTGATAACCCTGCCGCAGCGGCGAAATTATTACAGCAACTACAAccgc                      >  2:1108583/1‑76 (MQ=255)                                             ggCTTTTTCGCGATTGGGATGCAA‑GGTTGATAGCCCTGCCGCAGCGGCGAAATTATTACAGGaa                                <  1:673289/64‑1 (MQ=255)                                             ggCTTTTTCGCGACTGGGATGCAA‑GGTTGATAACCCTGCCGCAGCGGCGAAATTATTACAGGaa                                >  2:673289/1‑64 (MQ=255)                                             ggCTTTTTCGCGACTGGGATGCAA‑GGTTGATAACCCTGCCGCAGCGGCGAAATTATTACAGGAACTACAAccgccg                    >  1:1237342/1‑76 (MQ=255)                                             ggCTTTTTCGCGACTGGGATGCAA‑GGTTGATAACCCTGCCGCAGCGGCGAAATTATTACAGGAACTACAAccgccg                    >  1:439721/1‑76 (MQ=255)                                                tttttCGCGACTGGGATGCAA‑GGTTGATAACCCTGCCGCAGCGGCGAAATTATTACAGGAACTACAACCGCCGGtt                 >  1:1336041/1‑76 (MQ=255)                                                ttgttCGGGACGGGGA‑GGAAGGGTTAATACCCCTGCCGCAGCGGCGAAATTATTACAGGAACTACAACCGCCGGtt                 <  1:1387332/73‑1 (MQ=255)                                                 tttcCGCGGCGGGGATG‑AAAGGTTGATACCCCTGCCGCAGCGGCGAAATTATTACAGAAACTACAACCGCCGGTTc                <  2:220796/76‑1 (MQ=255)                                                  tttCGCGACTGGGATGCAA‑GGTTGATAACCCTGCCGCAGCGGCGAAATTATTACAGGAACTACAACCGCCGGTTca               >  2:1428766/1‑76 (MQ=255)                                                  tttCGCGACTGGGATGCAA‑GGTTGATAACCCTGCCGCAGCGGCGAAATTATTACAGGAACTACAACCGCCGGTTca               >  1:54175/1‑76 (MQ=255)                                                   ttCGCGACTGGGATGCAA‑GGTTGATAACCCTGCCGCAGCGGCGAAATTATTACAGGAACTACAACCGCCGGTTcag              >  2:65046/1‑76 (MQ=255)                                                    tCGCGACTGGGATGCAA‑GGTTGATAACCCTGCCGCAGCGGCGAAATTATTACAGGAACTACAACCGCCGGTTcagc             >  2:1296398/1‑76 (MQ=255)                                                       cgACTGGGATGCAA‑GGTTGATAACCCTGCCGCAGCGGCGAAATTATTACAGGAACTACAACCGCCGGTTCAGCAgg          >  2:1374961/1‑76 (MQ=255)                                                           tGGGATGCAA‑GGTTGATAACCCTGCCGCAGCGGCGAAATTATTACAGGAACTACAACCGCCGGTTCAGCAGGTGAt      >  2:492109/1‑76 (MQ=255)                                                           tGGGATGCAA‑GGTTGATAACCCTGCCGCAGCGGCGAAATTATTACAGGAACTACAACCGCCGGTTCAGCAGGTGAt      >  1:873900/1‑76 (MQ=255)                                                            gggATGCAA‑GGTTGATAACCCTGCCGCAGCGGCGAAATTATTACAGGAACTACAACCGCCGGTTCAGCAGGTGAtt     >  2:185081/1‑76 (MQ=255)                                                            gggATGCAA‑GGTTGATAACCCTGCCGCAGCGGCGAAATTATTACAGGAACTACAACCGCCGGTTCAGCAGGTGAtt     >  2:498587/1‑76 (MQ=255)                                                              gATGCAA‑GGTTGATAACCCTGCCGCAGCGGCGAAATTATTACAGGAACTACAACCGCCGGTTCAGCAGGTGATTTc   >  2:926100/1‑76 (MQ=255)                                                               aTGCAA‑GGTTGATAACCCTGCCGCAGCGGCGAAATTATTACAGGAACTACAACCGCCGGTTCAGCAGGTGATTTcc  >  1:1521112/1‑76 (MQ=255)                                                                     |                                                                       TCTCTATCCCAGCATGTTTAATTCGCGCGTTGAGGAAGAGGAAAGGCTTTTTCGCGACTGGGATGCAATGGTTGATAACCCTGCCGCAGCGGCGAAATTATTACAGGAACTACAACCGCCGGTTCAGCAGGTGATTTCC  >  REL606/1290404‑1290542

Alignment Legend
Aligned base mismatch/match (shaded by quality score): ATCG/ATCG < 3 ≤ ATCG/ATCG < 25 ≤ ATCG/ATCG < 30 ≤ ATCG/ATCG < 36 ≤ ATCG/ATCG < 38 ≤ ATCG/ATCG
Unaligned base: atcg    Masked matching base: atcg    Alignment gap: ‑    Deleted base: ‑