Predicted mutation
evidence	seq id	position	mutation	annotation	gene	description
RA	NC_000913	257,794	T→C	intergenic (+23/‑35)	frsA → / → crl	fermentation‑respiration switch protein/RNA polymerase holoenzyme assembly factor Crl

Read alignment evidence...
	seq id	position		ref	new	freq	score (cons/poly)	reads	annotation	genes	product
*	NC_000913	257,794	0	T	C	100.0%	350.7 / NA	83	intergenic (+23/‑35)	frsA/crl	fermentation‑respiration switch protein/RNA polymerase holoenzyme assembly factor Crl
Reads supporting (aligned to +/- strand):  ref base T (0/0);  new base C (41/42);  total (41/42)

CTTGTGTTAAAAATTTGCTAAATTTTGCCAATTTGGTAAAACAGTTGCATCACAACAGGAGA  >  NC_000913/257762‑257823                                 |                              cTTGTGTTAAAAATTTGCTAAATTTTGCCAATCTg                             >  1:4980006/1‑35 (MQ=255)  ttGTGTTAAAAATTTGCTAAATTTTGCCAATCTgg                            <  1:7817211/35‑1 (MQ=255)  ttGTGTTAAAAATTTGCTAAATTTTGCCAATCTgg                            >  1:1872206/1‑35 (MQ=38)  ttGTGTTAAAAATTTGCTAAATTTTGCCAATCTgg                            <  1:6519412/35‑1 (MQ=255)  ttGTGTTAAAAATTTGCTAAATTTTGCCAATCTgg                            <  1:5697413/35‑1 (MQ=38)   tgtgTTAAAAATTTGCTAAATTTTGCCAATCTGGt                           >  1:1028770/1‑35 (MQ=255)   tgtgTTAAAAATTTGCTAAATTTTGCCAATCTGGt                           >  1:2610017/1‑35 (MQ=255)   tgtgTTAAAAATTTGCTAAATTTTGCCAATCTGGt                           <  1:7861660/35‑1 (MQ=255)   tgtgTTAAAAATTTGCTAAATTTTGCCAATCTGGt                           <  1:5828757/35‑1 (MQ=38)   tgtgTTAAAAATTTGCTAAATTTTGCCAATCTGGt                           <  1:6279355/35‑1 (MQ=38)    gtgtTAAAAATTTGCTAAATTTTGCCAATCTGGTa                          >  1:5905919/1‑35 (MQ=255)    gtgtTAAAAATTTGCTAAATTTTGCCAATCTGGTa                          <  1:1843766/35‑1 (MQ=38)    gtgtTAAAAATTTGCTAAATTTTGCCAATCTGGTa                          <  1:4360566/35‑1 (MQ=38)    gtgtTAAAAATTTGCTAAATTTTGCCAATCTGGTa                          <  1:3950136/35‑1 (MQ=255)     tgtTAAAAATTTGCTAAATTTTGCCAATCTGGTaa                         <  1:4736116/35‑1 (MQ=255)     tgtTAAAAATTTGCTAAATTTTGCCAATCTGGTaa                         >  1:2476101/1‑35 (MQ=38)     tgtTAAAAATTTGCTAAATTTTGCCAATCTGGTaa                         >  1:2558428/1‑35 (MQ=255)     tgtTAAAAATTTGCTAAATTTTGCCAATCTGGTaa                         >  1:3063714/1‑35 (MQ=255)      gtTAAAAATTTGCTAAATTTTGCCAATCTGGTaaa                        <  1:6673993/35‑1 (MQ=255)      gtTAAAAATTTGCTAAATTTTGCCAATCTGGTaaa                        <  1:3308789/35‑1 (MQ=255)      gtTAAAAATTTGCTAAATTTTGCCAATCTGGTaaa                        <  1:3112794/35‑1 (MQ=255)       ttAAAAATTTGCTAAATTTTGCCAATCTGGTaaaa                       <  1:7277927/35‑1 (MQ=255)       ttAAAAATTTGCTAAATTTTGCCAATCTGGTaaaa                       <  1:7286805/35‑1 (MQ=38)        tAAAAATTTGCTAAATTTTGCCAATCTGGTAAAAc                      >  1:7375213/1‑35 (MQ=38)         aaaaaTTTGCTAAATTTTGCCAATCTGGTAAAACa                     >  1:5953198/1‑35 (MQ=38)         aaaaaTTTGCTAAATTTTGCCAATCTGGTAAAACa                     >  1:7281894/1‑35 (MQ=255)         aaaaaTTTGCTAAATTTTGCCAATCTGGTAAAACa                     >  1:1192920/1‑35 (MQ=38)         aaaaaTTTGCTAAATTTTGCCAATCTGGTAAAACa                     >  1:1308467/1‑35 (MQ=255)         aaaaaTTTGCTAAATTTTGCCAATCTGGTAAAACa                     >  1:6597465/1‑35 (MQ=255)          aaaaTTTGCTAAATTTTGCCAATCTGGTAAAACAg                    >  1:2143485/1‑35 (MQ=38)          aaaaTTTGCTAAATTTTGCCAATCTGGTAAAACAg                    >  1:2434797/1‑35 (MQ=38)           aaaTTTGCTAAATTTTGCCAATCTGGTAAAACAGt                   <  1:5252656/35‑1 (MQ=255)             aTTTGCTAAATTTTGCCAATCTGGTAAAACAGTTg                 <  1:295686/35‑1 (MQ=255)             aTTTGCTAAATTTTGCCAATCTGGTAAAACAGTTg                 <  1:5955297/35‑1 (MQ=38)             aTTTGCTAAATTTTGCCAATCTGGTAAAACAGTTg                 <  1:4220896/35‑1 (MQ=38)              tttGCTAAATTTTGCCAATCTGGTAAAACAGTTGc                >  1:4915735/1‑35 (MQ=38)              tttGCTAAATTTTGCCAATCTGGTAAAACAGTTGc                >  1:7602811/1‑35 (MQ=255)               ttGCTAAATTTTGCCAATCTGGTAAAACAGTTGCa               >  1:2915703/1‑35 (MQ=38)               ttGCTAAATTTTGCCAATCTGGTAAAACAGTTGCa               <  1:6577258/35‑1 (MQ=255)               ttGCTAAATTTTGCCAATCTGGTAAAACAGTTGCa               >  1:6470594/1‑35 (MQ=255)                tGCTAAATTTTGCCAATCTGGTAAAACAGTTGCAt              >  1:6795318/1‑35 (MQ=38)                tGCTAAATTTTGCCAATCTGGTAAAACAGTTGCAt              <  1:1274690/35‑1 (MQ=255)                tGCTAAATTTTGCCAATCTGGTAAAACAGTTGCAt              >  1:805357/1‑35 (MQ=255)                tGCTAAATTTTGCCAATCTGGTAAAACAGTTGCAt              >  1:1364588/1‑35 (MQ=38)                 gCTAAATTTTGCCGATCTGGTAAAACAGTTGCATc             <  1:6910670/35‑1 (MQ=25)                 gCTAAATTTTGCCAATCTGGTAAAACAGTTGCATc             >  1:7850487/1‑35 (MQ=255)                 gCTAAATTTTGCCAATCTGGTAAAACAGTTGCATc             <  1:6616997/35‑1 (MQ=38)                 gCTAAATTTTGCCAATCTGGTAAAACAGTTGCATc             <  1:5844151/35‑1 (MQ=255)                 gCTAAATTTTGCCAATCTGGTAAAACAGTTGCATc             >  1:5304801/1‑35 (MQ=255)                  cTAAATTTTGCCAATCTGGTAAAACAGTTGCATca            <  1:4095192/35‑1 (MQ=255)                  cTAAATTTTGCCAATCTGGTAAAACAGTTGCATca            <  1:5983431/35‑1 (MQ=255)                  cTAAATTTTGCCAATCTGGTAAAACAGTTGCATca            >  1:3072645/1‑35 (MQ=255)                  cTAAATTTTGCCAATCTGGTAAAACAGTTGCATca            <  1:177241/35‑1 (MQ=255)                  cTAAATTTTGCCAATCTGGTAAAACAGTTGCATca            <  1:364034/35‑1 (MQ=255)                   tAAATTTTGCCAATCTGGTAAAACAGTTGCATcac           <  1:7228402/35‑1 (MQ=38)                   tAAATTTTGCCAATCTGGTAAAACAGTTGCATcac           <  1:2647548/35‑1 (MQ=255)                     aaTTTTGCCAATCTGGTAAAACAGTTGCATCacaa         <  1:2957832/35‑1 (MQ=255)                     aaTTTTGCCAATCTGGTAAAACAGTTGCATCacaa         >  1:7890450/1‑35 (MQ=255)                     aaTTTTGCCAATCTGGTAAAACAGTTGCATCacaa         <  1:4555183/35‑1 (MQ=255)                     aaTTTTGCCAATCTGGTAAAACAGTTGCATCacaa         <  1:2262225/35‑1 (MQ=255)                     aaTTTTGCCAATCTGGTAAAACAGTTGCATCacaa         <  1:4195104/35‑1 (MQ=38)                     aaTTTTGCCAATCTGGTAAAACAGTTGCATCacaa         >  1:4162415/1‑35 (MQ=38)                     aaTTTTGCCAATCTGGTAAAACAGTTGCATCacaa         >  1:7852489/1‑35 (MQ=38)                      aTTTTGCCAATCTGGTAAAACAGTTGCATCacaac        >  1:4566132/1‑35 (MQ=255)                       ttttGCCAATCTGGTAAAACAGTTGCATCacaaca       >  1:5936563/1‑35 (MQ=255)                       ttttGCCAATCTGGTAAAACAGTTGCATCacaaca       >  1:6050829/1‑35 (MQ=38)                       ttttGCCAATCTGGTAAAACAGTTGCATCacaaca       >  1:4938899/1‑35 (MQ=255)                        tttGCCAATCTGGTAAAACAGTTGCATCACAACAg      <  1:1583781/35‑1 (MQ=255)                        tttGCCAATCTGGTAAAACAGTTGCATCACAACAg      <  1:1171759/35‑1 (MQ=255)                        tttGCCAATCTGGTAAAACAGTTGCATCACAACAg      <  1:3095059/35‑1 (MQ=255)                        tttGCCAATCTGGTAAAACAGTTGCATCACAACAg      <  1:2726777/35‑1 (MQ=255)                        tttGCCAATCTGGTAAAACAGTTGCATCACAACAg      <  1:3131769/35‑1 (MQ=38)                        tttGCCAATCTGGTAAAACAGTTGCATCACAACAg      <  1:1738066/35‑1 (MQ=255)                         ttGCCAATCTGGTAAAACAGTTGCATCACAACAgg     >  1:849760/1‑35 (MQ=38)                         ttGCCAATCTGGTAAAACAGTTGCATCACAACAgg     >  1:1093263/1‑35 (MQ=38)                          tGCCAATCTGGTAAAACAGTTGCATCACAACAGga    >  1:2071711/1‑35 (MQ=38)                           gCCAATCTGGTAAAACAGTTGCATCACAACAGgag   >  1:5614075/1‑35 (MQ=255)                           gCCAATCTGGTAAAACAGTTGCATCACAACAGgag   >  1:434236/1‑35 (MQ=255)                           gCCAATCTGGTAAAACAGTTGCATCACAACAGgag   >  1:3393465/1‑35 (MQ=38)                            ccAATCTGGTAAAACAGTTGCATCACAACAGgaga  <  1:7293602/35‑1 (MQ=38)                            ccAATCTGGTAAAACAGTTGCATCACAACAGgaga  <  1:3562304/35‑1 (MQ=255)                            ccAATCTGGTAAAACAGTTGCATCACAACAGgaga  >  1:1981812/1‑35 (MQ=255)                            ccAATCTGGTAAAACAGTTGCATCACAACAGgaga  >  1:1695711/1‑35 (MQ=255)                                 |                              CTTGTGTTAAAAATTTGCTAAATTTTGCCAATTTGGTAAAACAGTTGCATCACAACAGGAGA  >  NC_000913/257762‑257823

Alignment Legend
Aligned base mismatch/match (shaded by quality score): ATCG/ATCG < 3 ≤ ATCG/ATCG < 25 ≤ ATCG/ATCG < 32 ≤ ATCG/ATCG < 38 ≤ ATCG/ATCG < 40 ≤ ATCG/ATCG
Unaligned base: atcg    Masked matching base: atcg    Alignment gap: ‑    Deleted base: ‑