Sample Resequencing Stats

Note: The mutation counts shown below represent unfiltered mutation sets.
ALE, Flask, Isolate Predicted Mutations Mean Coverage Total Reads Percent Mapped Mapped Reads Average Read Length
A5 F1 I2 R1 772 77.0 3769570 91.6% 3452926 105.3

Breseq alignment

BRESEQ :: Evidence
Predicted mutation
evidence seq id position mutation annotation gene description
RA NC_000913 1,920,205 (T)7→8 intergenic (+62/‑18) yebT → / → rsmF MCE domain protein/16S rRNA m(5)C1407 methyltransferase, SAM‑dependent

Read alignment evidence...
  seq id position ref new freq score (cons/poly) reads annotation genes product
*NC_0009131,920,1981.T98.1% 164.6 / ‑3.8 52intergenic (+55/‑25)yebT/rsmFMCE domain protein/16S rRNA m(5)C1407 methyltransferase, SAM‑dependent
Reads supporting (aligned to +/- strand):  ref base . (0/1);  new base T (27/24);  total (27/25)
Fisher's exact test for biased strand distribution p-value = 4.81e-01
Kolmogorov-Smirnov test that lower quality scores support variant p-value = 9.13e-01

GGAAGGCAAACACTTCCTGTTGCAGGAAAGTGAACCGAAAGAGTGGCGTGAATGGGGAACTGCGCTTCCCAAATAATGCCCACTGCTCCGGCGTGCCTGCGCCGGAGCGTTTATGCTAAACTGCGCGCCTG‑TTTT‑TTTGCCAGTGGTACATGCTCGTGGCCCAACACACCGTTTATTTCCCGGACGCCTTTCTGACACAAATGCGCGAAGCGATGCCTTCGACGCTCTCATTTGATGATTTTCTTGCCGCCTGTCAGCGCC  >  NC_000913/1920068‑1920328
                                                                                                                                   |                                                                                                                                   
ggAAGGCAAACACTTCCTGTTGCAGGAAAGTGAACCGAAAGAGTGGCGTGAATGGGGAACTGCGCTTCCCAAATAATGCCCACTGCTCCGGCGTGCCTGCGCCGGAGCGTTTATGCTAAACTGCGCGCCTG‑tttt‑tttt                                                                                                                            <  1:1476366/139‑2 (MQ=255)
ggAAGGCAAACACTTCCTGTTGCAGGAAAGTGAACCGAAAGAGTGGCGTGAATGGGGAACTGCGCTTCCCAAATAATGCCCACTGCTCCGGCGTGCCTGCGCCGGAGCGTTTATGCTAAACTGCGCGCCTG‑tttt‑tttt                                                                                                                            >  1:388773/1‑138 (MQ=255)
  aaGGCAAACACTTCCTGTTGCAGGAAAGTGAACCGAAAGAGTGGCGTGAATGGGGAACTGCGCTTCCCAAATAATGCCCACTGCTCCGGCGTGCCTGCGCCGGAGCGTTTATGCTAAACTGCGCGCCTG‑tttt‑ttttgc                                                                                                                          <  2:388773/139‑4 (MQ=255)
     gCAAACACTTCCTGTTGCAGGAAAGTGAACCGAAAGAGTGGCGTGAATGGGGAACTGCGCTTCCCAAATAATGCCCACTGCTCCGGCGTGCCTGAGCCGGAGCGTTTATGCTAAACTGCGCGCCTGTTTTT‑TTTGCCAg                                                                                                                        <  1:1329451/139‑1 (MQ=255)
         acacTTCCTGTTGCAGGAAAGTGAACCGAAAGAGTGGCGTGAATGGGGAACTGCGCTTCCCAAATAATGCCCACTGCTCCGGCGTGCCTGCGCCGGAGCGTTTATGCTAAACTGCGCGCCTG‑tttt‑ttttgcc                                                                                                                         <  2:691996/133‑5 (MQ=255)
         acacTTCCTGTTGCAGGAAAGTGAACCGAAAGAGTGGCGTGAATGGGGAACTGCGCTTCCCAAATAATGCCCACTGCTCCGGCGTGCCTGCGCCGGAGCGTTTATGCTAAACTGCGCGCCTG‑tttt‑ttttgcc                                                                                                                         >  1:691996/1‑129 (MQ=255)
            cTTCCTGTTGCAGGAAAGTGAACCGAAAGAGTGGCGTGAATGGGGAACTGCGCTTCCCAAATAATGCCCACTGCTCCGGCGTGCCTGCGCCGGAGCGTTTATGCTAAACTGCGCGCCTGTTTTT‑TTTGCCAGTGGTACa                                                                                                                 <  2:365695/139‑1 (MQ=255)
               ccTGTTGCAGGAAAGTGAACCGAAAGAGTGGCGTGAATGGGGAACTGCGCTTCCCAAATAATGCCCACTGCTCCGGCGTGCCTGCGCCGGAGCGTTTATGCTAAACTGCGCGCCTGTTTTT‑TTTGCCAGTGGTACATGc                                                                                                              >  1:593002/1‑139 (MQ=255)
                      cAGGAAAGTGAACCGAAAGAGTGGCGTGAATGGGGAACTGCGCTTCCCAAATAATGCCCACTGCTCCGGCGTGCCTGCGCCGGAGCGTTTATGCTAAACTGCGCGCCTGTTTTT‑TTTGCCAGTGGTACATGCTCGTGGc                                                                                                       <  1:829/139‑1 (MQ=255)
                            aGTGAACCGAAAGAGTGGCGTGAATGGGGAACTGCGCTTCCCAAATAATGCCCACTGCTCCGGCGTGCCTGCGCCGGAGCGTTTATGCTAAACTGCGCGCCTGTTTTT‑TTTGCCAGTGGTACATGCTCGTGGCCCAaca                                                                                                 <  1:1518526/139‑1 (MQ=255)
                                aaCCGAAAGAGTGGCGTGAATGGGGAACTGCGCTTCCCAAATAATGCCCACTGCTCCGGCGTGCCTGCGCCGGAGCGTTTATGCTAAACTGCGCGCCTG‑tttt‑ttttgcca                                                                                                                        >  2:597033/1‑106 (MQ=255)
                                aaCCGAAAGAGTGGCGTGAATGGGGAACTGCGCTTCCCAAATAATGCCCACTGCTCCGGCGTGCCTGCGCCGGAGCGTTTATGCTAAACTGCGCGCCTG‑tttt‑ttttgcca                                                                                                                        <  1:597033/111‑6 (MQ=255)
                                        gagTGGCGTGAATGGGGAACTGCGCTTCCCAAATAATGCCCACTGCTCCGGCGTGCCTGCGCCGGAGCGTTTATGCTAAACTGCGCGCCTGTTTTT‑TTTGCCAGTGGTACATGCTCGTGGCCCAACACACCGTTTAttt                                                                                     >  2:1199493/1‑139 (MQ=255)
                                               gTGAATGGGGAACTGCGCTTCCCAAATAATGCCCACTGCTCCGGCGTGCCTGCGCCGGAGCGTTTATGCTAAACTGCGCGCCTGTTTTT‑TTTGCCAGTGGTACATGCTCGTGGCCCAACACACCGTTTATTTCCCGGAc                                                                              <  1:517826/139‑1 (MQ=255)
                                                tGAATGGGGAACTGAGCTTCCCAAATAATGCCCACTGCTCCGGCGTGCCTGCGCCGGAGCGTCTATGCTAAACTGCGCCCCTG‑TTTTCTTTGCCAGTGGTACATGCTCGTGGCCGAACACACCGTTTATTTCCCGGACg                                                                             <  2:1149262/139‑1 (MQ=255)
                                                        gAACTGCGCTTCCCAAATAATGCCCACTGCTCCGGCGTGCCTGCGCCGGAGCGTTTATGCTAAACTGCGCGCCTG‑tttt‑ttttgc                                                                                                                          <  1:1734066/85‑4 (MQ=255)
                                                        gAACTGCGCTTCCCAAATAATGCCCACTGCTCCGGCGTGCCTGCGCCGGAGCGTTTATGCTAAACTGCGCGCCTG‑tttt‑ttttgc                                                                                                                          >  2:1734066/1‑82 (MQ=255)
                                                           cTGCGCTTCCCAAATAATGCCCACTGCTCCGGCGTGCCTGCGCCGGAGCGTTTATGCTAAACTGCGCGCCTGTTTTT‑TTTGCCAGTGGTACATGCTCGTGGCCCAACACACCGTTTATTTCCCGGACGCCTTTc                                                                       >  1:353188/1‑134 (MQ=255)
                                                           cTGCGCTTCCCAAATAATGCCCACTGCTCCGGCGTGCCTGCGCCGGAGCGTTTATGCTAAACTGCGCGCCTGTTTTT‑TTTGCCAGTGGTACATGCTCGTGGCCCAACACACCGTTTATTTCCCGGACGCCTTTc                                                                       <  2:353188/134‑1 (MQ=255)
                                                            tGCGCTTCCCAAATAATGCCCACTGCTCCGGCGTGCCTGCGCCGGAGCGTTTATGCTAAACTGCGCGCCTGTTTTT‑TTTGCCAGTGGTACATGCTCGTGGCCCAACACACCGTTTATTTCCCGGACGCCTTTCTGacac                                                                 >  2:521394/1‑139 (MQ=255)
                                                             gcgcTTCCCAAATAATGCCCACTGCTCCGGCGTGCCTGCGCCGGAGCGTTTATGCTAAACTGCGCGCCTGTTTTT‑TTTGCCAGTGGTACATGCTCGTGGCCCAACACACCGTTTATTTCCCGGACGCCTTTCTGAcaca                                                                >  2:1457423/1‑139 (MQ=255)
                                                              cgcTTCCCAAATAATGCCCACTGCTCCGGCGTGCCTGCGCCGGAGCGTTTATGCTAAACTGCGCGCCTGTTTTT‑TTTGCCAGTGGTACATGCTCGTGGCCCAACACACCGTTTATTTCCCGGACGCCTTTCTGACACaa                                                               >  1:1278764/1‑139 (MQ=255)
                                                                   cccAAATAATGCCCACTGCTCCGGCGTGCCTGCGCCGGAGCGTTTATGCTAAACTGCGCGCCTGTTTTT‑TTTGCCAGTGGTACATGCTCGTGGCCCAACACACCGTTTATTTCCCGGACGCCTTTCTGACACAAATgcg                                                          <  1:1199493/139‑1 (MQ=255)
                                                                    ccAAATAATGCCCACTGCTCCGGCGTGCCTGCGCCGGAGCGTTTATGCTAAACTGCGCGCCTGTTTTT‑TTTGCCAGTGGTACATGCTCGTGGCCCAACACACCGTTTATTTCCCGGACGCCTTTCTGACACAAATgcgc                                                         <  1:521394/139‑1 (MQ=255)
                                                                             gCCCACTGCTCCGGCGTGCCTGCGCCGGAGCGTTTATGCTAAACTGCGCGCCTGTTTTT‑TTTGCCAGTGGTACATGCTCGTGGccc                                                                                                     >  2:26448/1‑86 (MQ=255)
                                                                             gCCCACTGCTCCGGCGTGCCTGCGCCGGAGCGTTTATGCTAAACTGCGCGCCTGTTTTT‑TTTGCCAGTGGTACATGCTCGTGGccc                                                                                                     <  1:26448/86‑1 (MQ=255)
                                                                             gCCCACTGCTCCGGCGTGCCTGCGCCGGAGCGTTTATGCTAAACTGCGCGCCTGTTTTT‑TTTGCCAGTGGTACATGCTCGTGGCCCAACACACCGTTTATTTCCCGGACGCCTTTCTGACACAAATGCGCGAAGCg                                                   >  1:1486284/1‑136 (MQ=255)
                                                                             gCCCACTGCTCCGGCGTGCCTGCGCCGGAGCGTTTATGCTAAACTGCGCGCCTGTTTTT‑TTTGCCAGTGGTACATGCTCGTGGCCCAACACACCGTTTATTTCCCGGACGCCTTTCTGACACAAATGCGCGAAGCg                                                   <  2:1486284/136‑1 (MQ=255)
                                                                             gCCCACTGCTCCGGCGTGCCTGCGCCGGAGCGTTTATGCTAAACTGCGCGCCTGTTTTT‑TTTGCCAGTGGTACATGCTCGTGGCCCAACACACCGTTTATTTCCCGGACGCCTTTCTGACACAAATGCGCGAAGCGATg                                                >  1:549988/1‑139 (MQ=255)
                                                                             gCCCACTGCTCCGGCGTGCCTGCGCCGGAGCGTTTATGCTAAACTGCGCGCCTGTTTTT‑TTTGCCAGTGGTACATGCTCGTGGCCCAACACACCGTTTATTTCCCGGACGCCTTTCTGACACAAATGCGCGAAGCGATg                                                >  2:377509/1‑139 (MQ=255)
                                                                              cccACTGCTCCGGCGTGCCTGCGCCGGAGCGTTTATGCTAAACTGCGCGCCTGTTTTT‑TTTGCCAGTGGTACATGCTCGTGGCCCAacacac                                                                                              >  1:1341442/1‑92 (MQ=255)
                                                                              cccACTGCTCCGGCGTGCCTGCGCCGGAGCGTTTATGCTAAACTGCGCGCCTGTTTTT‑TTTGCCAGTGGTACATGCTCGTGGCCCAacacac                                                                                              <  2:1341442/92‑1 (MQ=255)
                                                                                  cTGCTCCGGCGTGCCTGCGCCGGAGCGTTTATGCTAAACTGCGCGCCTG‑tttt‑tttt                                                                                                                            >  2:932068/1‑56 (MQ=255)
                                                                                  cTGCTCCGGCGTGCCTGCGCCGGAGCGTTTATGCTAAACTGCGCGCCTG‑tttt‑tttt                                                                                                                            <  1:932068/57‑2 (MQ=255)
                                                                                   tGCTCCGGCGTGCCTGCGCCGGAGCGTTTATGCTAAACTGCGCGCCTGTTTTT‑TTTGCCAGTGGTACATGCTCGTGGCCCAACACACCGTTTATTTCCCGGACGCCTTTCTGACACAAATGCGCGAAGCGATGCCTTCg                                          >  1:1206997/1‑139 (MQ=255)
                                                                                     cTCCGGCGTGCCTGCGCCGGAGCGTTTATGCTAAACTGCGCGCCTGTTTTT‑TTTGCCAGTGGTACATGCTCGTGGCCCAACACACCGTTTATTTCCCGGACGCCTTTCTGACACAAATGCGCGAAGCGATGCCTTCGAc                                        >  2:152183/1‑139 (MQ=255)
                                                                                      tCCGGCGTGCCTGCGCCGGAGCGTTTATGCTAAACTGCGCGCCTGTTTTT‑TTTGCCAGTGGTACATGCTCGTGGCCCAACACACCGTTTATTTCCCGGACGCCTTTCTGACACAAATGCGCGAAGCGATGCCTTCGACg                                       <  2:1206997/139‑1 (MQ=255)
                                                                                              gCCTGCGCCGGAGCGTTTATGCTAAACTGCGCGCCTGTTTTT‑TTTGCCAGTGGTACATGCTCGTGGCCCAACACACCGTTTATTTCCCGGACGCCTTTCTGACACAAATGCGCGAAGCGATGCCTTCGACGCTCTCAtt                               <  2:1278764/139‑1 (MQ=255)
                                                                                               cccgcgcCGGAGCGTTTATGCTAAACTGCGCGCCTGTTTTT‑TTTGCCAGTGGTACATGCTCGTGGCCCAACACACCGTTTATTTCCCGGACGCCTTTCTGACACAAATGCGCGAAGCGATGCCTTCg                                          >  1:1068601/4‑127 (MQ=255)
                                                                                               cccgcgcCGGAGCGTTTATGCTAAACTGCGCGCCTGTTTTT‑TTTGCCAGTGGTACATGCTCGTGGCCCAACACACCGTTTATTTCCCGGACGCCTTTCTGACACAAATGCGCGAAGCGATGCCTTCg                                          <  2:1068601/124‑1 (MQ=255)
                                                                                               ccTGCGCCGGAGCGTTTATGCTAAACTGCGCGCCTGTTTTT‑TTTGCCAGTGGTACATGCTCGTGGCCCAACACACCGTTTATTTCCCGGACGCCTTTCTGACACAAATGCGCGAAGc                                                    >  1:660934/1‑117 (MQ=255)
                                                                                               ccTGCGCCGGAGCGTTTATGCTAAACTGCGCGCCTGTTTTT‑TTTGCCAGTGGTACATGCTCGTGGCCCAACACACCGTTTATTTCCCGGACGCCTTTCTGACACAAATGCGCGAAGc                                                    <  2:660934/117‑1 (MQ=255)
                                                                                               ccTGCGCCGGAGCGTTTATGCTAAACTGCGCGCCTGTTTTT‑TTTGCCAGTGGTACATGCTCGTGGCCCAACACACCGTTTATTTCCCGGACGCCTTTCTGACACAAATGCGCGAAGCGATGCCTTCGACGCTCTCAttt                              >  1:1131196/1‑139 (MQ=255)
                                                                                                cTGCGCCGGAGCGTTTATGCTAAACTGCGCGCCTGTTTTT‑TTTGCCAGTGGTACATGCTCGTGGCCCAACACACCGTTTATTTCCCgg                                                                                <  1:196587/88‑1 (MQ=255)
                                                                                                cTGCGCCGGAGCGTTTATGCTAAACTGCGCGCCTGTTTTT‑TTTGCCAGTGGTACATGCTCGTGGCCCAACACACCGTTTATTTCCCgg                                                                                >  2:196587/1‑88 (MQ=255)
                                                                                                         aGCGTTTATGCTAAACTGCGCGCCTGTTTTT‑TTTGCCAGTGGTACATGCTCGTGGCCCa                                                                                                    <  2:1091103/59‑1 (MQ=255)
                                                                                                         aGCGTTTATGCTAAACTGCGCGCCTGTTTTT‑TTTGCCAGTGGTACATGCTCGTGGCCCAaca                                                                                                 >  2:663574/1‑62 (MQ=255)
                                                                                                         aGCGTTTATGCTAAACTGCGCGCCTGTTTTT‑TTTGCCAGTGGTACATGCTCGTGGCCCAaca                                                                                                 <  1:663574/62‑1 (MQ=255)
                                                                                                         aGCGTTTATGCTAAACTGCGCGCCTGTTTTT‑TTTGCCAGTGGTACATGCTCGTGGCCCAACACACCGTTTAt                                                                                       >  1:546828/1‑72 (MQ=255)
                                                                                                         aGCGTTTATGCTAAACTGCGCGCCTGTTTTT‑TTTGCCAGTGGTACATGCTCGTGGCCCAACACACCGTTTAt                                                                                       <  2:546828/72‑1 (MQ=255)
                                                                                                         aGCGTTTATGCTAAACTGCGCGCCTGTTTTT‑TTTGCCAGTGGTACATGCTCGTGGCCCAACACACCGTTTATTTCCCg                                                                                 >  1:402473/1‑78 (MQ=255)
                                                                                                         aGCGTTTATGCTAAACTGCGCGCCTGTTTTT‑TTTGCCAGTGGTACATGCTCGTGGCCCAACACACCGTTTATTTCCCg                                                                                 <  2:402473/78‑1 (MQ=255)
                                                                                                         aGCGATTATGCAAAACTGCGCGCCTGTTTTT‑TTTGCCAGTGGTACATGCTCGTGGCCCa                                                                                                    >  1:1091103/1‑59 (MQ=255)
                                                                                                                     aaaCTGCGCGCCTGTTTTT‑TTTGCCAGTGGTACATGCTCGTGGCCCAACACACCGTTTATTTCCCGGACGCCTTTCTGACACAAATGCGCGAAGCGATGCCTTCGACGCTCTCATTtgat                           <  2:1659978/120‑1 (MQ=255)
                                                                                                                     aaaCTGCGCGCCTGTTTTT‑TTTGCCAGTGGTACATGCTCGTGGCCCAACACACCGTTTATTTCCCGGACGCCTTTCTGACACAAATGCGCGAAGCGATGCCTTCGACGCTCTCATTtgat                           >  1:1659978/1‑120 (MQ=255)
                                                                                                                         tGCGCGCCTGTTTTT‑TTTGCCAGTGGTACATGCTCGTGGCCCAACACACCGTTTATTTCCCGGACGCCTTTCTGACACAAATGCGCGAAGCGATGCCTTCGACGCTCTCATTTGATGATTTTCTTGCCGCCTGTCAgcg    <  1:377509/139‑1 (MQ=255)
                                                                                                                           cgcgcCTGTTTTT‑TTTGCCAGTGGTACATGCTCGTGGCCCAaca                                                                                                 >  1:1007889/1‑44 (MQ=38)
                                                                                                                           cgcgcCTGTTTTT‑TTTGCCAGTGGTACATGCTCGTGGCCCAaca                                                                                                 <  2:1007889/44‑1 (MQ=255)
                                                                                                                           cgcgcCTGTTTTT‑TTTGCCAGTGGTACATGCTCGTGGCCCAACACACCGTTTATTTCCCGGACGCCTTTCTGACACAAATGCGCGAAGCGATGCCTTCGACGCTCTCATTTGATGATTTTCTTGCCGCCTGTCAGCGcc  >  1:1575716/1‑139 (MQ=255)
                                                                                                                           cgcgcCTGTTTTT‑TTTGCCAGTGGTACATGCTCGTGGCCCAACACACCGTTTATTTCCCGGACGCCTTTCTGACACAAATGCGCGAAGCGATGCCTTCGACGCTCTCATTTGATGATTTTCTTGCCGCCTGTCAGCGcc  >  2:1093551/1‑139 (MQ=255)
                                                                                                                           cgcgcCTGTTTTT‑TTTGCCAGTGGTACATGCTCGTGGCCCAACACACCGTTTATTTCCCGGACGCCTTTCTGACACAAATGCGCGAAGCGATGCCTTCGACGCTCTCATTTGATGATTTTCTTGCCGCCTGTCAGCGcc  >  1:954460/1‑139 (MQ=255)
                                                                                                                             cgcCTGTTTTT‑TTTGCCAGTGGTACATGCTCGTGGCCCAACACACCGTTTAt                                                                                       >  1:1533601/1‑52 (MQ=255)
                                                                                                                             cgcCTGTTTTT‑TTTGCCAGTGGTACATGCTCGTGGCCCAACACACCGTTTAt                                                                                       <  2:1533601/52‑1 (MQ=255)
                                                                                                                                   |                                                                                                                                   
GGAAGGCAAACACTTCCTGTTGCAGGAAAGTGAACCGAAAGAGTGGCGTGAATGGGGAACTGCGCTTCCCAAATAATGCCCACTGCTCCGGCGTGCCTGCGCCGGAGCGTTTATGCTAAACTGCGCGCCTG‑TTTT‑TTTGCCAGTGGTACATGCTCGTGGCCCAACACACCGTTTATTTCCCGGACGCCTTTCTGACACAAATGCGCGAAGCGATGCCTTCGACGCTCTCATTTGATGATTTTCTTGCCGCCTGTCAGCGCC  >  NC_000913/1920068‑1920328

Alignment Legend
Aligned base mismatch/match (shaded by quality score): ATCG/ATCG < 3 ≤ ATCG/ATCG < 27 ≤ ATCG/ATCG < 35 ≤ ATCG/ATCG < 39 ≤ ATCG/ATCG < 40 ≤ ATCG/ATCG
Unaligned base: atcg    Masked matching base: atcg    Alignment gap: ‑    Deleted base: ‑

GATK/CNVnator alignment

N/A