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
A11 F1 I1 R1 757 76.1 3598070 93.4% 3360597 108.6

Breseq alignment

BRESEQ :: Evidence
Predicted mutation
evidence seq id position mutation annotation gene description
RA NC_000913 4,353,081 G→A *58* (TAG→TAA)  ghoT → toxin of GhoTS toxin‑antitoxin pair, membrane‑lytic protein, stimulator of persister cell formation

Read alignment evidence...
  seq id position ref new freq score (cons/poly) reads annotation genes product
*NC_0009134,353,0810GA100.0% 182.5 / NA 56*58* (TAG→TAA) ghoTtoxin of GhoTS toxin‑antitoxin pair, membrane‑lytic protein, stimulator of persister cell formation
Reads supporting (aligned to +/- strand):  ref base G (0/0);  new base A (30/26);  total (30/26)

ATCCTTTGTCATTATCTGGTTTATCTCACATGAGAAAACACATATTCGTTTACTTAGTGCATTCCTGGTCGGAATAACCTGGCCAATGAGTCTGCCTGTGGCATTACTTTTTTCTCTCTTTTAGGAGCTGTAGTTGAGTGGACCCGCTGGTTATCGTGAAACGAAGCGTCTCTCCTCAAAACTGGATTTGCGGAACGATGAACGAAGCAGTCGCCTGACTGCTTCGTTCATTAAAGTGAAATTTATTTC  >  NC_000913/4352958‑4353206
                                                                                                                           |                                                                                                                             
atCCTTTGTCATTATCTGGTTTATCTCACATGAGAAAACACATATTCGTTTACTTAGTGCATTCCTGGTCGGAATAACCTGGCCAATGAGTCTGCCTGTGGCATTACTTTTTTCTCTCTTTTAagag                                                                                                                            >  1:418810/1‑127 (MQ=255)
atCCTTTGTCATTATCTGGTTTATCTCACATGAGAAAACACATATTCGTTTACTTAGTGCATTCCTGGTCGGAATAACCTGGCCAATGAGTCTGCCTGTGGCATTACTTTTTTCTCTCTTTTAagag                                                                                                                            <  2:418810/127‑1 (MQ=255)
     ttGTCATTATCTGGTTTATCTCACATGAGAAAACACATATTCGTTTACTTAGTGCATTCCTGGTCGGAATAACCTGGCCAATGAGTCTGCCTGTGGCATTACTTTTTTCTCTCTTTTAagag                                                                                                                            <  1:60004/122‑1 (MQ=255)
     ttGTCATTATCTGGTTTATCTCACATGAGAAAACACATATTCGTTTACTTAGTGCATTCCTGGTCGGAATAACCTGGCCAATGAGTCTGCCTGTGGCATTACTTTTTTCTCTCTTTTAagag                                                                                                                            >  2:60004/1‑122 (MQ=255)
     ttGTCATTATCTGGTTTATCTCACATGAGAAAACACATATTCGTTTACTTAGTGCATTCCTGGTCGGAATAACCTGGCCAATGAGTCTGCCTGTGGCATTACTTTTTTCTCTCTTTTAAGAGCTGTAGTTGAGTGGAcc                                                                                                           >  2:950854/1‑139 (MQ=255)
     ttGTCATTATCTGGTTTATCTCACATGAGAAAACACATATTCGTTTACTTAGTGCATTCCTGGTCGGAATAACCTGGCCAATGAGTCTGCCTGTGGCATTACTTTTTTCTCTCTTTTAAGAGCTGTAGTTGAGTGGAcc                                                                                                           >  1:132732/1‑139 (MQ=255)
           ttATCTGGTTTATCTCACATGAGAAAACACATATTCGTTTACTTAGTGCATTCCTGGTCGGAATAACCTGGCCAATGAGTCTGCCTGTGGCATTACTTTTTTCTCTCTTTTAagag                                                                                                                            >  2:1456849/1‑116 (MQ=255)
           ttATCTGGTTTATCTCACATGAGAAAACACATATTCGTTTACTTAGTGCATTCCTGGTCGGAATAACCTGGCCAATGAGTCTGCCTGTGGCATTACTTTTTTCTCTCTTTTAagag                                                                                                                            <  1:1456849/116‑1 (MQ=255)
            tATCTGGTTTATCTCACATGAGAAAACACATATTCGTTTACTTAGTGCATTCCTGGTCGGAATAACCTGGCCAATGAGTCTGCCTGTGGCATTACTTTTTTCTCTCTTTTAAGAGCTGTAGTTGAGTGGACCCGCTGGt                                                                                                    >  2:1103548/1‑139 (MQ=255)
             aTCTGGTTTATCTCACATGAGAAAACACATATTCGTTTACTTAGTGCATTCCTGGTCGGAATAACCTGGCCAATGAGTCTGCCTGTGGCATTACTTTTTTCTCTCTTTTAAGAGCTGTAGTTGAGTGGACCCGCTGGtt                                                                                                   >  2:1623034/1‑139 (MQ=255)
             aTCTGGTTTATCTCACATGAGAAAACACATATTCGTTTACTTAGTGCATTCCTGGTCGGAATAACCTGGCCAATGAGTCTGCCTGTGGCATTACTTTTTTCTCTCTTTTAAGAGCTGTAGTTGAGTGGACCCGCTGGtt                                                                                                   >  2:44868/1‑139 (MQ=255)
                  gTTTATCTCACATGAGAAAACACATATTCGTTTACTTAGTGCATTCCTGGTCGGAATAACCTGGCCAATGAGTCTGCCTGTGGCATTACTTTTTTCTCTCTTTTAAGAGCTGTAGTTGAGTGGACCCGCTGGTTATCGt                                                                                              >  1:1766228/1‑139 (MQ=255)
                        ctcACATGAGAAAACACATATTCGTTTACTTAGTGCATTCCTGGTCGGAATAACCTGGCCAATGAGTCTGCCTGTGGCATTACTTTTTTCTCTCTTTTAAGAGCTGTAGTTGAGTGGACCCGCTGGTTATCGTGaa                                                                                           >  2:1670344/1‑136 (MQ=255)
                        ctcACATGAGAAAACACATATTCGTTTACTTAGTGCATTCCTGGTCGGAATAACCTGGCCAATGAGTCTGCCTGTGGCATTACTTTTTTCTCTCTTTTAAGAGCTGTAGTTGAGTGGACCCGCTGGTTATCGTGaa                                                                                           <  1:1670344/136‑1 (MQ=255)
                           acaTGAGAAAACACATATTCGTTTACTTAGTGCATTCCTGGTCGGAATAACCTGGCCAATGAGTCTGCCTGTGGCATTACTTTTTTCTCTCTTTTAAGAGCTGTAGTTGAGTGGACCCGCTGGTTATCGTGAAACGAAg                                                                                     <  2:1766228/139‑1 (MQ=255)
                           acaTGAGAAAACACATATTCGTTTACTTAGTGCATTCCTGGTCGGAATAACCTGGCCAATGAGTCTGCCTGTGGCATTACTTTTTTCTCTCTTTTAAGAGCTGTAGTTGAGTGGACCCGCTGGTTATCGTGAAACGAAg                                                                                     <  1:1363202/139‑1 (MQ=255)
                            caTGAGAAAACACATATTCGTTTACTTAGTGCATTCCTGGTCGGAATAACCTGGCCAATGAGTCTGCCTGTGGCATTACTTTTTTCTCTCTTTTAAGAGCTGTAGTTGAGTgg                                                                                                              <  2:654418/113‑1 (MQ=255)
                            caTGAGAAAACACATATTCGTTTACTTAGTGCATTCCTGGTCGGAATAACCTGGCCAATGAGTCTGCCTGTGGCATTACTTTTTTCTCTCTTTTAAGAGCTGTAGTTGAGTgg                                                                                                              >  1:654418/1‑113 (MQ=255)
                            caTGAGAAAACACATATTCGTTTACTTAGTGCATTCCTGGTCGGAATAACCTGGCCAATGAGTCTGCCTGTGGCATTACTTTTTTCTCTCTTTTAAGAGCTGTAGTTGAGTGGa                                                                                                             <  1:1604016/114‑1 (MQ=255)
                            caTGAGAAAACACATATTCGTTTACTTAGTGCATTCCTGGTCGGAATAACCTGGCCAATGAGTCTGCCTGTGGCATTACTTTTTTCTCTCTTTTAAGAGCTGTAGTTGAGTGGa                                                                                                             >  2:1604016/1‑114 (MQ=255)
                            caTGAGAAAACACATATTCGTTTACTTAGTGCATTCCTGGTCGGAATAACCTGGCCAATGAGTCTGCCTGTGGCATTACTTTTTTCTCTCTTTTAAGAGCTGTAGTTGAGTGGACCCGCTGGt                                                                                                    >  2:335033/1‑123 (MQ=255)
                            caTGAGAAAACACATATTCGTTTACTTAGTGCATTCCTGGTCGGAATAACCTGGCCAATGAGTCTGCCTGTGGCATTACTTTTTTCTCTCTTTTAAGAGCTGTAGTTGAGTGGACCCGCTGGt                                                                                                    <  1:335033/123‑1 (MQ=255)
                            caTGAGAAAACACATATTCGTTTACTTAGTGCATTCCTGGTCGGAATAACCTGGCCAATGAGTCTGCCTGTGGCATTACTTTTTTCTCTCTTTTAAGAGCTGTAGTTGAGTGGACCCGCTGGTTATCGTGAAACGAAGc                                                                                    >  1:1023002/1‑139 (MQ=255)
                            caTGAGAAAACACATATTCGTTTACTTAGTGCATTCCTGGTCGGAATAACCTGGCCAATGAGTCTGCCTGTGGCATTACTTTTTTCTCTCTTTTAAGAGCTGTAGTTGAGTGGACCCGCTGGTTATCGTGAAACGAAGc                                                                                    >  1:92637/1‑139 (MQ=255)
                              tGAGAAAACACATATTCGTTTACTTAGTGCATTCCTGGTCGGAATAACCTGGCCAATGAGTCTGCCTGTGGCATTACTTTTTTCTCTCTTTTAAGAGCTGTAGTTGAGTGGACCCGCTGGTTATCGTGAAACGAAGCGt                                                                                  <  2:132732/139‑1 (MQ=255)
                                      cacaTATTCGTTTACTTAGTGCATTCCTGGTCGGAATAACCTGGCCAATGAGTCTGCCTGTGGCATTACTTTTTTCTCTCTTTTAAGAGCTGTAGTTGAGTGGACCCGCTGGTTATCGTGAAACGAAGCGTCTctcctc                                                                          <  1:950854/139‑1 (MQ=255)
                                       acaTATTCGTTTACTTAGTGCATTCCTGGTCGGAATAACCTGGCCAATGAGTCTGCCTGTGGCATTACTTTTTTCTCTCTTTTAAGAGCTGTAGTTGAGTGGACCCGCTGGTTATCGTGAAACGAAGCGtct                                                                                <  1:1230198/132‑1 (MQ=255)
                                       acaTATTCGTTTACTTAGTGCATTCCTGGTCGGAATAACCTGGCCAATGAGTCTGCCTGTGGCATTACTTTTTTCTCTCTTTTAAGAGCTGTAGTTGAGTGGACCCGCTGGTTATCGTGAAACGAAGCGtct                                                                                >  2:1230198/1‑132 (MQ=255)
                                                           cATTCCTGGTCGGAATAACCTGGCCAATGAGTCTGCCTGTGGCATTACTTTTTTCTCTCTTTTAAGAGCTGTAGTTGAGTGGACCCGCTGGTTATCGTGAAACGAAGCGTCTCTCCTCAAAACTGGATTTGCGGAACg                                                      >  2:1373039/1‑138 (MQ=255)
                                                           cATTCCTGGTCGGAATAACCTGGCCAATGAGTCTGCCTGTGGCATTACTTTTTTCTCTCTTTTAAGAGCTGTAGTTGAGTGGACCCGCTGGTTATCGTGAAACGAAGCGTCTCTCCTCAAAACTGGATTTGCGGAACg                                                      <  1:1373039/138‑1 (MQ=255)
                                                              tCCTGGTCGGAATAACCTGGCCAATGAGTCTGCCTGTGGCATTACTTTTTTCTCTCTTTTAAGAGCTGTAGTTGAGTGGACCCGCTGGTTATCGTGAAACGAAGCGTCTCTCCTCAAAACTGGATTTGCGGAACGATGa                                                  >  2:955966/1‑139 (MQ=255)
                                                              tCCTGGTCGGAATAACCTGGCCAATGAGTCTGCCTGTGGCATTACTTTTTTCTCTCTTTTAAGAGCTGTAGTTGAGTGGACCCGCTGGTTATCGTGAAACGAAGCGTCTCTCCTCAAAACTGGATTTGCGGAACGATGa                                                  >  1:1212413/1‑139 (MQ=255)
                                                                 tGGTCGGAATAACCTGGCCAATGAGTCTGCCTGTGGCATTACTTTTTTCTCTCTTTTAAGAGCTGTAGTTGAGTGGACCCGCTGGTTATCGTGAAACGAAGCGTCTCTCCTCAAAACTGGATTTGCGGAACGATGAACg                                               <  1:1623034/139‑1 (MQ=255)
                                                                     cGGAATAACCTGGCCAATGAGTCTGCCTGTGGCATTACTTTTTTCTCTCTTTTAAGAGCTGTAGTTGAGTGGACCCGCTGGTTATCGTGAAACGAAGCGTCTCTCCTCAAAACTGGATTTGCGGAACGATGAACGAAGc                                           <  1:955966/139‑1 (MQ=255)
                                                                        aaTAACCTGGCCAATGAGTCTGCCTGTGGCATTACTTTTTTCTCTCTTTTAAGAGCTGTAGTTGAGTg                                                                                                               <  1:1510196/68‑1 (MQ=255)
                                                                        aaTAACCTGGCCAATGAGTCTGCCTGTGGCATTACTTTTTTCTCTCTTTTAAGAGCTGTAGTTGAGTg                                                                                                               >  2:1510196/1‑68 (MQ=255)
                                                                        aaTAACCTGGCCAATGAGTCTGCCTGTGGCATTACTTTTTTCTCTCTTTTAAGAGCTGTAGTTGAGTGGACCCGCTGGTTATCGTGAAACGAAGCGTCTCTCCTCAAAACTGGATTTGCGGAACGATGAACGAAGCAGt                                        >  2:119149/1‑139 (MQ=255)
                                                                             ccTGGCCAATGAGTCTGCCTGTGGCATTACTTTTTTCTCTCTTTTAAGAGCTGTAGTTGAGTGGACCCGCTGGTTATCGTGAAACGAAGCGTCTCTCCTCAAAACTGGATTTGCGGAACg                                                      >  2:1459081/1‑120 (MQ=255)
                                                                             ccTGGCCAATGAGTCTGCCTGTGGCATTACTTTTTTCTCTCTTTTAAGAGCTGTAGTTGAGTGGACCCGCTGGTTATCGTGAAACGAAGCGTCTCTCCTCAAAACTGGATTTGCGGAACg                                                      <  1:1459081/120‑1 (MQ=255)
                                                                              cTGGCCAATGAGTCTGCCTGTGGCATTACTTTTTTCTCTCTTTTAAGAGCTGTAGTTGAGTGGACCCGCTGGTTATCGTGAAACGAAGCGTCTCTCCTCAAAACTGGATTTGCGGAACGATGAACGAAGCAGTCGCCTg                                  <  2:1023002/139‑1 (MQ=255)
                                                                                  ccAATGAGTCTGCCTGTGGCATTACTTTTTTCTCTCTTTTAAGAGCTGTAGTTGAGTGGACCCGCTgg                                                                                                     <  2:1426057/68‑1 (MQ=255)
                                                                                  ccAATGAGTCTGCCTGTGGCATTACTTTTTTCTCTCTTTTAAGAGCTGTAGTTGAGTGGACCCGCTgg                                                                                                     >  1:1426057/1‑68 (MQ=255)
                                                                                    aaTGAGTCTGCCTGTGGCATTACTTTTTTCTCTCTTTTAAGAGCTGTAGTTGAGTGGACCCGCTGGTTATCGTGAAACGAAGCGTCTCTCCTCAAAACTGGATTTGCGGAACGATGAACGAAGCAGTCGCCTGACTGCt                            <  2:92637/139‑1 (MQ=255)
                                                                                      tGAGTCTGCCTGTGGCATTACTTTTTTCTCTCTTTTAAGAGCTGTAGTTGAGTgg                                                                                                              >  2:1507558/1‑55 (MQ=255)
                                                                                      tGAGTCTGCCTGTGGCATTACTTTTTTCTCTCTTTTAAGAGCTGTAGTTGAGTgg                                                                                                              <  1:1507558/55‑1 (MQ=255)
                                                                                      tGAGTCTGCCTGTGGCATTACTTTTTTCTCTCTTTTAAGAGCTGTAGTTGAGTGGACCCGCTGGt                                                                                                    >  1:1291536/1‑65 (MQ=255)
                                                                                      tGAGTCTGCCTGTGGCATTACTTTTTTCTCTCTTTTAAGAGCTGTAGTTGAGTGGACCCGCTGGt                                                                                                    <  2:1291536/65‑1 (MQ=255)
                                                                                      tGAGTCTGCCTGTGGCATTACTTTTTTCTCTCTTTTAAGAGCTGTAGTTGAGTGGACCCGCTGGTTATCGTGAAACGAAGCGTCTctcctc                                                                          <  2:133149/91‑1 (MQ=255)
                                                                                      tGAGTCTGCCTGTGGCATTACTTTTTTCTCTCTTTTAAGAGCTGTAGTTGAGTGGACCCGCTGGTTATCGTGAAACGAAGCGTCTctcctc                                                                          >  1:133149/1‑91 (MQ=255)
                                                                                                  tgGCATTACTTTTTTCTCTCTTTTAAGAGCTGTAGTTGAGTGGACCCGCTGGTTATCGTGAAACGAAGCGTCTCTCCTCAAAACTGGAt                                                                <  1:417712/89‑1 (MQ=255)
                                                                                                  tgGCATTACTTTTTTCTCTCTTTTAAGAGCTGTAGTTGAGTGGACCCGCTGGTTATCGTGAAACGAAGCGTCTCTCCTCAAAACTGGAt                                                                >  2:417712/1‑89 (MQ=255)
                                                                                                    gCATTACTTTTTTCTCTCTTTTAAGAGCTGTAGTTGAGTGGACCCGCTGGTTATCGTGAAACGAAGCGTCTCTCCTCAAAACTGGATTTGCGGAACGATGAACGAAGCAGt                                        <  2:1255532/111‑1 (MQ=255)
                                                                                                    gCATTACTTTTTTCTCTCTTTTAAGAGCTGTAGTTGAGTGGACCCGCTGGTTATCGTGAAACGAAGCGTCTCTCCTCAAAACTGGATTTGCGGAACGATGAACGAAGCAGt                                        >  1:1255532/1‑111 (MQ=255)
                                                                                                              tttCTCTCTTTTAAGAGCTGTAGTTGAGTGGACCCGCTGGTTATCGTGAAACGAAGCGTCTCTCCTCAAAACTGGATTTGCGGAACGATGAACGAAGCAGTCGCCTGACTGCTTCGTTCATTAAAGTGAAATTTATTTc  >  2:439162/1‑139 (MQ=255)
                                                                                                               ttCTCTCTTTTAAGAGCTGTAGTTGAGTGGACCCGCTGGTTATCGTGAAACGAAg                                                                                     <  2:688206/55‑1 (MQ=255)
                                                                                                               ttCTCTCTTTTAAGAGCTGTAGTTGAGTGGACCCGCTGGTTATCGTGAAACGAAg                                                                                     >  1:688206/1‑55 (MQ=255)
                                                                                                                    tctTTTAAGAGCTGTAGTTGAGTGGACCCGCTGGTTATCGTGAAACGAAGCGTCTCTCCTCAAAACTGGATTTGCGGAACGATGAACGAAGCAGTCg                                      >  2:820960/1‑97 (MQ=255)
                                                                                                                    tctTTTAAGAGCTGTAGTTGAGTGGACCCGCTGGTTATCGTGAAACGAAGCGTCTCTCCTCAAAACTGGATTTGCGGAACGATGAACGAAGCAGTCg                                      <  1:820960/97‑1 (MQ=255)
                                                                                                                    tctTTTAAGAGCTGTAGTTGAGTGGACCCGCTGGTTATCGTGAAACGAAGCGTCTCTCCTCAAAACTGGATTTGCGGAACGATGAACGAAGCAGTCGCCTGACTGCTTCGTTCATTAAAGTGaa           <  2:562299/124‑1 (MQ=255)
                                                                                                                    tctTTTAAGAGCTGTAGTTGAGTGGACCCGCTGGTTATCGTGAAACGAAGCGTCTCTCCTCAAAACTGGATTTGCGGAACGATGAACGAAGCAGTCGCCTGACTGCTTCGTTCATTAAAGTGaa           >  1:562299/1‑124 (MQ=255)
                                                                                                                     ctTTTAAGAGCTGTAGTTGAGTGGACCCGCTGGTTATCGTGAAACGAAGCGt                                                                                  <  2:275354/52‑1 (MQ=255)
                                                                                                                     ctTTTAAGAGCTGTAGTTGAGTGGACCCGCTGGTTATCGTGAAACGAAGCGt                                                                                  >  1:275354/1‑52 (MQ=255)
                                                                                                                           |                                                                                                                             
ATCCTTTGTCATTATCTGGTTTATCTCACATGAGAAAACACATATTCGTTTACTTAGTGCATTCCTGGTCGGAATAACCTGGCCAATGAGTCTGCCTGTGGCATTACTTTTTTCTCTCTTTTAGGAGCTGTAGTTGAGTGGACCCGCTGGTTATCGTGAAACGAAGCGTCTCTCCTCAAAACTGGATTTGCGGAACGATGAACGAAGCAGTCGCCTGACTGCTTCGTTCATTAAAGTGAAATTTATTTC  >  NC_000913/4352958‑4353206

Alignment Legend
Aligned base mismatch/match (shaded by quality score): ATCG/ATCG < 3 ≤ ATCG/ATCG < 34 ≤ ATCG/ATCG < 37 ≤ ATCG/ATCG < 39 ≤ ATCG/ATCG < 40 ≤ ATCG/ATCG
Unaligned base: atcg    Masked matching base: atcg    Alignment gap: ‑    Deleted base: ‑

GATK/CNVnator alignment

N/A