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
A8 F1 I2 R1 765 53.2 2691310 93.4% 2513683 103.8

Breseq alignment

BRESEQ :: Evidence
Predicted mutation
evidence seq id position mutation annotation gene description
RA NC_000913 3,466,313 A→G L138P (CTT→CCT)  bfr ← bacterioferritin, iron storage and detoxification protein

Read alignment evidence...
  seq id position ref new freq score (cons/poly) reads annotation genes product
*NC_0009133,466,3130AG98.4% 213.8 / ‑5.5 61L138P (CTT→CCT) bfrbacterioferritin, iron storage and detoxification protein
Reads supporting (aligned to +/- strand):  ref base A (0/0);  major base G (32/28);  minor base C (0/1);  total (32/29)
Fisher's exact test for biased strand distribution p-value = 4.75e-01
Kolmogorov-Smirnov test that lower quality scores support variant p-value = 9.95e-01

AGCATGATAAACCTGGGGTATCTGGCCTGGATCTCTTATTAACCGGGAGGGTTCTCCCTCCCGACACGGCTCAACCTTCTTCGCGGATCTGTGCTTGCAGATAATTTTGCAGGCCCATCTTCTGAATCAGATCAAGTTCCGTTTCCAGCCAGTCGATATGGCCTTCTTCATCACGCAAAATTTCTATCATCATATCGCGGCTGACGTAATCATGAACGCTATCGGCATAACCAATTGCCTCACGCAAATTCTTCGCGCCATCCAGCTCA  >  NC_000913/3466179‑3466447
                                                                                                                                      |                                                                                                                                      
agcaTGATAAACCTGGGGTATCTGGCCTGGATCTCTTATTAACCGGGAGGGTTCTCCCTCCCGACACGGCTCAACCTTCTTCGCGGATCTGTGCTTGCAGATAATTTTGCAGGCCCATCTTCTGAATCAGATCAGGTTc                                                                                                                                    <  2:644973/139‑1 (MQ=255)
            cTGGGGTATCTGGCCTGGATCTCTTATTAACCGGGAGGGTTCTCCCTCCCGACACGGCTCAACCTTCTTCGCGGATCTGTGCTTGCAGATAATTTTGCAGGCCCATCTTCTGAATCAGATCAGGTTCCGTTTccagcca                                                                                                                        <  1:451806/139‑1 (MQ=255)
                    tCTGGCCTGGATCTCTTATTAACCGGGAGGGTTCTCCCTCCCGACACGGCTCAACCTTCTTCGCGGATCTGTGCTTGCAGATAATTTTGCAGGCCCATCTTCTGAATCAGATCAGGtt                                                                                                                                     >  2:1248600/1‑118 (MQ=255)
                    tCTGGCCTGGATCTCTTATTAACCGGGAGGGTTCTCCCTCCCGACACGGCTCAACCTTCTTCGCGGATCTGTGCTTGCAGATAATTTTGCAGGCCCATCTTCTGAATCAGATCAGGtt                                                                                                                                     <  1:1248600/118‑1 (MQ=255)
                     cTGGCCTGGATCTCTTATTAACCGGGAGGGTTCTCCCTCCCGACACGGCTCAACCTTCTTCGCGGATCTGTGCTTGCAGATAATTTTGCAGGCCCATCTTCTGAATCAGATCAGGtt                                                                                                                                     <  2:1033339/117‑1 (MQ=255)
                     cTGGCCTGGATCTCTTATTAACCGGGAGGGTTCTCCCTCCCGACACGGCTCAACCTTCTTCGCGGATCTGTGCTTGCAGATAATTTTGCAGGCCCATCTTCTGAATCAGATCAGGtt                                                                                                                                     >  1:1033339/1‑117 (MQ=255)
                     cTGGCCTGGATCTCTTATTAACCGGGAGGGTTCTCCCTCCCGACACGGCTCAACCTTCTTCGCGGATCTGTGCTTGCAGATAATTTTGCAGGCCCATCTTCTGAATCAGATCAGGTTCCGTTTCCAGCCAGTCGATATg                                                                                                               <  2:475709/139‑1 (MQ=255)
                                  ctTATTAACCGGGAGGGTTCTCCCTCCCGACACGGCTCAACCTTCTTCGCGGATCTGTGCTTGCAGATAATTTTGCAGGCCCATCTTCTGAATCAGATCAGGTTCCGTTTCCAGCCAGTCGATATGGCCTTCTtcatca                                                                                                  >  2:392992/1‑139 (MQ=255)
                                     attaACCGGGAGGGTTCTCCCTCCCGACACGGCTCAACCTTCTTCGCGGATCTGTGCTTGCAGATAATTTTGCAGGCCCATCTTCTGAATCAGATCAGGTTCCGTTTCCAGCCAGTCGATATGGCCTTCTTCATCACGc                                                                                               <  1:98292/139‑1 (MQ=255)
                                         aCCGGGAGGGTTCTCCCTCCCGACACGGCTCAACCTTCTTCGCGGATCTGTGCTTGCAGATAATTTTGCAGGCCCATCTTCTGAATCAGATCAGGTTCCGTTTCCAGCCAGTCGATATg                                                                                                               <  1:154816/119‑1 (MQ=255)
                                         aCCGGGAGGGTTCTCCCTCCCGACACGGCTCAACCTTCTTCGCGGATCTGTGCTTGCAGATAATTTTGCAGGCCCATCTTCTGAATCAGATCAGGTTCCGTTTCCAGCCAGTCGATATg                                                                                                               >  2:154816/1‑119 (MQ=255)
                                             ggAGTGTTCTCCCTCCCGACACGGCTCAACCTTCTTCGCGGATCTGTGCTTGCAGATAATTTTGCAGGCCCATCTTCTGAATCAGATCACGTTCCGTTTccagc                                                                                                                          <  1:817522/104‑1 (MQ=255)
                                             ggAGGGTTCTCCCTCCCGACACGGCTCAACCTTCTTCGCGGATCTGTGCTTGCAGATAATTTTGCAGGCCCATCTTCTGAATCAGATCAGGTTc                                                                                                                                    <  2:558302/94‑1 (MQ=255)
                                             ggAGGGTTCTCCCTCCCGACACGGCTCAACCTTCTTCGCGGATCTGTGCTTGCAGATAATTTTGCAGGCCCATCTTCTGAATCAGATCAGGTTc                                                                                                                                    >  1:558302/1‑94 (MQ=255)
                                             ggAGGGTTCTCCCTCCCGACACGGCTCAACCTTCTTCGCGGATCTGTGCTTGCAGATAATTTTGCAGGCCCATCTTCTGAATCAGATCAGGTTCCGTTTccagccag                                                                                                                       <  1:1102855/107‑1 (MQ=255)
                                             ggAGGGTTCTCCCTCCCGACACGGCTCAACCTTCTTCGCGGATCTGTGCTTGCAGATAATTTTGCAGGCCCATCTTCTGAATCAGATCAGGTTCCGTTTccagccag                                                                                                                       >  2:1102855/1‑107 (MQ=255)
                                             ggAGGGTTCTCCCTCCCGACACGGCTCAACCTTCTTCGCGGATCTGTGCTTGCAGATAATTTTGCAGGCCCATCTTCTGAATCAGATCAGGTTCCGTTTCCAGCCAGTCGATATgg                                                                                                              <  1:475739/116‑1 (MQ=255)
                                             ggAGGGTTCTCCCTCCCGACACGGCTCAACCTTCTTCGCGGATCTGTGCTTGCAGATAATTTTGCAGGCCCATCTTCTGAATCAGATCAGGTTCCGTTTCCAGCCAGTCGATATgg                                                                                                              >  2:475739/1‑116 (MQ=255)
                                             ggAGGGTTCTCCCTCCCGACACGGCTCAACCTTCTTCGCGGATCTGTGCTTGCAGATAATTTTGCAGGCCCATCTTCTGAATCAGATCAGGTTCCGTTTCCAGCCAGTCGATATGGCCTTCTTCATCACGCAAAATTTc                                                                                       >  1:445103/1‑139 (MQ=255)
                                             ggAGGGTTCTCCCTCCCGACACGGCTCAACCTTCTTCGCGGATCTGTGCTTGCAGATAATTTTGCAGGCCCATCTTCTGAATCAGATCAGGTTCCGTTTCCAGCCAGTCGATATGGCCTTCTTCATCACGCAAAATTTc                                                                                       >  2:1142649/1‑139 (MQ=255)
                                             ggAGGGTTCTCCCTCCCGACACGGCTCAACCTTCTTCGCGGATCTGTGCTTGCAGATAATTTTGCAGGCCCATCTTCTGAATCAGATCAGGTTCCGTTTCCACCCAGTCGATATGGCCTTCTTCATCACGCAAAATTTc                                                                                       >  2:94774/1‑139 (MQ=255)
                                             ggAGGGTTCTCCCTCCCGACACGGCTCAACCTTCTTCGCGGATCTGAGCTTGCAGATAATTTTGCAGGCCCATCTTCTGAATCAGATCAGGTTCCGTTTccagc                                                                                                                          >  2:817522/1‑104 (MQ=255)
                                               aGGGTTCTCCCTCCCGACACGGCTCAACCTTCTTCGCGGATCTGTGCTTGCAGATAATTTTGCAGGCCCATCTTCTGAATCAGATCAGGTTCCGTTTCCAGCCAGTCGata                                                                                                                 >  2:275714/1‑111 (MQ=255)
                                               aGGGTTCTCCCTCCCGACACGGCTCAACCTTCTTCGCGGATCTGTGCTTGCAGATAATTTTGCAGGCCCATCTTCTGAATCAGATCAGGTTCCGTTTCCAGCCAGTCGata                                                                                                                 <  1:275714/111‑1 (MQ=255)
                                               aGGGTTCTCCCTCCCGACACGGCTCAACCTTCTTCGCGGATCTGTGCTTGCAGATAATTTTGCAGGCCCATCTTCTGAATCAGATCAGGTTCCGTTTCCAGCCAGTCGATATGGCCTTCTTCATCACGCAAAATTTCTa                                                                                     >  2:331268/1‑139 (MQ=255)
                                               aGGGTTCTCCCTCCCGACACGGCTCAACCTTCTTCGCGGATCTGTGCTTGCAGATAATTTTGCAGGCCCATCTTCTGAATCAGATCAGGTTCCGTTTCCAGCCAGTCGATATGGCCTTCTTCATCACGCAAAATTTCTa                                                                                     <  1:597099/139‑1 (MQ=255)
                                                   ttCTCCCTCCCGACACGGCTCAACCTTCTTCGCGGATCTGTGCTTGCAGATAATTTTGCAGGCCCATCTTCTGAATCAGATCAGGTTCCGTTTCCAGCCAGTCGATATGGCCTTCTTCATCACGCAAAATTTCTa                                                                                     <  2:286635/135‑1 (MQ=255)
                                                   ttCTCCCTCCCGACACGGCTCAACCTTCTTCGCGGATCTGTGCTTGCAGATAATTTTGCAGGCCCATCTTCTGAATCAGATCAGGTTCCGTTTCCAGCCAGTCGATATGGCCTTCTTCATCACGCAAAATTTCTa                                                                                     >  1:286635/1‑135 (MQ=255)
                                                        cctcccGACACGGCTCAACCTTCTTCGCGGATCTGTGCTTGCAGATAATTTTGCAGGCCCATCTTCTGAATCAGATCAGGTTCCGTTTCCAGCCAGTCGATATGGCCTTCTTCATCACGCAAAATTTCTATCATCatat                                                                            <  2:445103/139‑1 (MQ=255)
                                                                     cTCAACCTTCTTCGCGGATCTGTGCTTGCAGATAATTTTGCAGGCCCATCTTCTGAATCAGATCAGGTTCCGTTTCCAGCCAGTCGATATGGCCTTCTTCATCACGCAAAATTTCTATCATCATATCGCGGCTGACGTa                                                               >  2:1296223/1‑139 (MQ=255)
                                                                             tcttcGCGGATCTGTGCTTGCAGATAATTTTGCAGGCCCATCTTCTGAATCAGATCAGGTTCCGTTTCCAGCCAGTCGATATGGCCTTCTTCATCACGCAAAATTTCTATCATCATATCGCGGCTGACGTAATCATGaa                                                       <  1:923875/139‑1 (MQ=255)
                                                                               ttcGCGGATCTGTGCTTGCAGATAATTTTGCAGGCCCATCTTCTGAATCAGATCAGGTTCCGTTTCCAGCCAGTCGATATGGCCTTCTTCATCACGCAAAATTTCTATCATCATATCGCGGCTGACGTAATCATGAACg                                                     >  1:276630/1‑139 (MQ=255)
                                                                                   cgGATCTGTGCTTGCAGATAATTTTGCAGGCCCATCTTCTGAATCAGATCAGGTTCCGTTTCCAGCCAGTCGATATGGCCTTCTTCATCACGCAAAATTTCTATCATCATATCGCGGCTGACGTAATCATGAACGCTAt                                                 <  2:276630/139‑1 (MQ=255)
                                                                                    ggATCTGTGCTTGCAGATAATTTTGCAGGCCCATCTTCTGAATCAGATCAGGTTCCGTTTCCAGCCAGTCGATATGGCCTTCTTCATCACGCAAAATTTCTatcat                                                                                 >  2:403639/1‑106 (MQ=255)
                                                                                    ggATCTGTGCTTGCAGATAATTTTGCAGGCCCATCTTCTGAATCAGATCAGGTTCCGTTTCCAGCCAGTCGATATGGCCTTCTTCATCACGCAAAATTTCTatcat                                                                                 <  1:403639/106‑1 (MQ=255)
                                                                                         tgtgCTTGCAGATAATTTTGCAGGCCCATCTTCTGAATCAGATCAGGTTCCGTTTCCAGCCAGTCGATATGGCCTTCTTCATCACGCAAAATTTCTATCATCATATCGCGGCTGACGTAATCATGAACGCTATCGGCAt                                           <  1:392992/139‑1 (MQ=255)
                                                                                         tgtgCTTGCAGATAATTTTGCAGGCCCATCTTCTGAATCAGATCAGGTTCCGTTTCCAGCCAGTCGATATGGCCTTCTTCATCACGCAAAATTTCTATCATCATATCGCGGCTGACGTAATCATGAACGCTATCGGCAt                                           <  1:331268/139‑1 (MQ=255)
                                                                                                gCAGATAATTTTGCAGGCCCATCTTCTGAATCAGATCAGGTTCCGTTTCCAGCCAGTCGATATGGCCTTCTTCATCACGCAAAATTTCTATCATCATATCGCGGCTGACGTAATCATGAACGCt                                                   >  1:253883/1‑124 (MQ=255)
                                                                                                gCAGATAATTTTGCAGGCCCATCTTCTGAATCAGATCAGGTTCCGTTTCCAGCCAGTCGATATGGCCTTCTTCATCACGCAAAATTTCTATCATCATATCGCGGCTGACGTAATCATGAACGCt                                                   <  2:253883/124‑1 (MQ=255)
                                                                                                gCAGATAATTTTGCAGGCCCATCTTCTGAATCAGATCAGGTTCCGTTTCCAGCCAGTCGATATGGCCTTCTTCATCACGCAAAATTTCTATCATCATATCGCGGCTGACGTAATCATGAACGCTATCGGCATAACCAAt                                    >  2:882065/1‑139 (MQ=255)
                                                                                                  aGATAATTTTGCAGGCCCATCTTCTGAATCAGATCAGGTTCCGTTTCCAGCCAGTCGATATGGCCTTCTTCATCACGCAAAATTTCTa                                                                                     >  1:1115894/1‑88 (MQ=255)
                                                                                                  aGATAATTTTGCAGGCCCATCTTCTGAATCAGATCAGGTTCCGTTTCCAGCCAGTCGATATGGCCTTCTTCATCACGCAAAATTTCTa                                                                                     <  2:1115894/88‑1 (MQ=255)
                                                                                                     tAATTTTGCAGGCCCATCTTCTGAATCAGATCAGGTTCCGTTTCCAGCCAGTCGATATGGCCTTCTTCATCACGCAAAATTTCTATCATCATATCGCGGCTGACGTAATCATg                                                         >  2:1014332/1‑113 (MQ=255)
                                                                                                     tAATTTTGCAGGCCCATCTTCTGAATCAGATCAGGTTCCGTTTCCAGCCAGTCGATATGGCCTTCGTCATCACGCAAAATTTCTATCATCATATCGCGGCTGACGTAATCATg                                                         <  1:1014332/113‑1 (MQ=255)
                                                                                                         tttGCAGGCCCATCTTCTGAATCAGATCAGGTTCCGTTTCCAGCCAGTCGATATGGCCTTCTTCATCACGCAAAATTTCTATCATCATATCGCGGCTGACGTAATCATGAACGCTATCGGCATAACCAATTGCCTCACg                           >  2:301157/1‑139 (MQ=255)
                                                                                                           tGCAGGCCCATCTTCTGAATCAGATCAGGTTCCGTTTCCAGCCAGTCGATATGGCCTTCTTCATCACGCAAAATTTCTATCATCATATCGCGGCTGACGTAATCATGAACGCTATCGGCATAACCAATTGCCTCACGCa                         >  1:1276518/1‑139 (MQ=255)
                                                                                                                gCCCATCTTCTGAATCAGATCAGGTTCCGTTTCCAGCCAGTCGATATGGCCTTCTTCATCACGCAAAATTTCTATCATCATATCGCGGCTGACGTAATCATGAACGCTATCGGCATAACCAATTGCCTCACGCAAAttc                    >  2:823308/1‑139 (MQ=255)
                                                                                                                  ccATCTTCTGAATCAGATCAGGTTCCGTTTCCAGCCAGTCGata                                                                                                                 <  1:389622/44‑1 (MQ=255)
                                                                                                                  ccATCTTCTGAATCAGATCAGGTTCCGTTTCCAGCCAGTCGata                                                                                                                 >  2:389622/1‑44 (MQ=255)
                                                                                                                  ccATCTTCTGAATCAGATCAGGTTCCGTTTCCAGCCAGTCGATATGGCCTTCTTCATCACGCAAAATTTc                                                                                       <  2:223821/70‑1 (MQ=255)
                                                                                                                  ccATCTTCTGAATCAGATCAGGTTCCGTTTCCAGCCAGTCGATATGGCCTTCTTCATCACGCAAAATTTc                                                                                       >  1:223821/1‑70 (MQ=255)
                                                                                                                     tcttctGAATCAGATCAGGTTCCGTTTCCAGCCAGTCGATATGGCCTTCTTCATCACGCAAAATTTCTATCATCATATCGCGGCTGACGTAATCATGAACGCTATCGGCATAACCAATTGCCTCACGCAAATTCTTcg                >  1:671726/1‑138 (MQ=255)
                                                                                                                     tcttctGAATCAGATCAGGTTCCGTTTCCAGCCAGTCGATATGGCCTTCTTCATCACGCAAAATTTCTATCATCATATCGCGGCTGACGTAATCATGAACGCTATCGGCATAACCAATTGCCTCACGCAAATTCTTcg                <  2:671726/138‑1 (MQ=255)
                                                                                                                      cttctGAATCAGATCAGGTTCCGTTTCCAGCCAGTCGATATGGCCTTCTTCATCACGCAAAATTTCTATCATCATATCGCGGCTGACGTAATCATGAACGCTATCGGCATAACCAATTGCCTCACGCAAATTCTTcgcg              <  1:823308/139‑1 (MQ=255)
                                                                                                                            aaTCAGATCAGGTTCCGTTTCCAGCCAGTCGATATGGCCTTCTTCATCACGCAAAATTTCTATCATCATATCGCGGCTGACGTAATCATGAACGCTATCGGCATAACCAATTGCCTCACGCAAATTCTTCGCGCCATcc        >  1:1014387/1‑139 (MQ=255)
                                                                                                                                 gATCAGGTTCCGTTTCCAGCCAGTCGATATGGCCTTCTTCATCACGCAAAATTTCTATCATCATATCGCGGc                                                                      <  2:1255861/72‑1 (MQ=255)
                                                                                                                                 gATCAGGTTCCGTTTCCAGCCAGTCGATATGGCCTTCTTCATCACGCAAAATTTCTATCATCATATCGCGGc                                                                      >  1:1255861/1‑72 (MQ=255)
                                                                                                                                 gATCAGGTTCCGTTTCCAGCCAGTCGATATGGCCTTCTTCATCACGCAAAATTTCTATCATCATATCGCGGCTGACGTAATCATGAACGCTATCGGCATAACCAATTGCCTCACGCAAATTCTTCGCGCCATCCAGCTc   >  2:1030850/1‑139 (MQ=255)
                                                                                                                                  aTCAGGTTCCGTTTCCAGCCAGTCGATATGGCCTTCTTCATCACGCAAAATTTCTATCATCATATCGCGGCTGACGTAATCATGAACGCTATCGGCATAACCAATTGCCt                               >  2:1049213/1‑110 (MQ=255)
                                                                                                                                  aTCAGGTTCCGTTTCCAGCCAGTCGATATGGCCTTCTTCATCACGCAAAATTTCTATCATCATATCGCGGCTGACGTAATCATGAACGCTATCGGCATAACCAATTGCCt                               <  1:1049213/110‑1 (MQ=255)
                                                                                                                                  aTCAGGTTCCGTTTCCAGCCAGTCGATATGGCCTTCTTCATCACGCAAAATTTCTATCATCATATCGCGGCTGACGTAATCATGAACGCTATCGGCATAACCAATTGCCTCACGCAAATTCTTCGCGCCATCCAGCTCa  >  2:1211706/1‑139 (MQ=255)
                                                                                                                                      |                                                                                                                                      
AGCATGATAAACCTGGGGTATCTGGCCTGGATCTCTTATTAACCGGGAGGGTTCTCCCTCCCGACACGGCTCAACCTTCTTCGCGGATCTGTGCTTGCAGATAATTTTGCAGGCCCATCTTCTGAATCAGATCAAGTTCCGTTTCCAGCCAGTCGATATGGCCTTCTTCATCACGCAAAATTTCTATCATCATATCGCGGCTGACGTAATCATGAACGCTATCGGCATAACCAATTGCCTCACGCAAATTCTTCGCGCCATCCAGCTCA  >  NC_000913/3466179‑3466447

Alignment Legend
Aligned base mismatch/match (shaded by quality score): ATCG/ATCG < 3 ≤ ATCG/ATCG < 27 ≤ ATCG/ATCG < 34 ≤ ATCG/ATCG < 39 ≤ ATCG/ATCG < 40 ≤ ATCG/ATCG
Unaligned base: atcg    Masked matching base: atcg    Alignment gap: ‑    Deleted base: ‑

GATK/CNVnator alignment

N/A