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
A2 F1 I0 R1 4577 57.4 3436498 77.7% 2670158 63.4

Breseq alignment

BRESEQ :: Evidence
Predicted mutation
evidence seq id position mutation freq annotation gene description
RA minE 2,796,501 T→C 40.0% N171N (AAT→AAC)  lexA → DNA‑binding transcriptional repressor

Read alignment evidence...
  seq id position ref new freq score (cons/poly) reads annotation genes product
*minE2,796,5010TC40.0% 54.1 / 89.7 125N171N (AAT→AAC) lexADNA‑binding transcriptional repressor
Reads supporting (aligned to +/- strand):  ref base T (54/21);  new base C (15/35);  total (69/56)
Fisher's exact test for biased strand distribution p-value = 4.20e-06
Kolmogorov-Smirnov test that lower quality scores support variant p-value = 1.00e+00

Only 100 of 132 total aligned reads displayed.

ATTGATGACGAAGTTACCGTTAAGCGCCTGAAAAAACAGGGCAATAAAGTCGAACTGTTGCCAGAAAATAGCGAGTTTAAACCAATTGTCGTTGACCTTCGTCAGCAGAGCTTCACCATTGAAGGGCTGGCGGT  >  minE/2796433‑2796566
                                                                    |                                                                 
aTTGATGACGAAGTTACCGTTAAGCGCCTGAAAAAACAGGGCAATAAAGTCTAACTGTTGCCAGAAAAt                                                                   <  1:2938015/69‑1 (MQ=255)
aTTGATGACGAAGTTACCGTTAAGCGCCTGAAAAAACAGGGCAATAAAGTCGAACTGTTGCCAGAAAAt                                                                   <  1:3052996/69‑1 (MQ=255)
aTTGATGACGAAGTTACCGTTAAGCGCCTGAAAAAACAGGGCAATAAAGTCGAACTGTTGCCAGAAAAt                                                                   <  1:1047698/69‑1 (MQ=255)
aTTGATGACGAAGTTACCGTTAAGCGCCTGAAAAAACAGGGCAATAAAGTCGAACTGTTGCCAGAAAAt                                                                   <  1:1867173/69‑1 (MQ=255)
aTTGATGACGAAGTTACCGTTAAGCGCCTGAAAAAACAGGGCAATAAAGTCGAACTGTTGCCAGAAAAt                                                                   <  1:3214159/69‑1 (MQ=255)
aTTGATGACGAAGTTACCGTTAAGCGCCTGAAAAAACAGGGCAATAAAGTCGAACTGTTGCCAGAAAAt                                                                   <  1:516725/69‑1 (MQ=255)
   gatgaCGAAGTTACCGTTAAGCGCCTGAAAAAACAGGGCAATAAATTCGAACTGTTGCCAGAAAATa                                                                  >  1:27724/1‑67 (MQ=255)
      gaCGAAGTTACCGTTAAACGGCTGAAAAAACAGGGCAATAAAGTCGAACTGTTGCCAGAAAACAGCGAg                                                             <  1:682582/69‑1 (MQ=39)
      gaCGAAGTTACCGTTAAACGCCTGAAAAAACAGGGCAATAATGTCGAACTGTTGCCAGAAAACAGCGAg                                                             <  1:114752/69‑1 (MQ=39)
      gaCGAAGTTACCGTTAAACGCCTGAAAAAACAGGGCAATAAAGTCGAACTGTTGCCAGAAAACAGCGAg                                                             <  1:3377522/69‑1 (MQ=255)
      gaCGAAGTTACCGTTAAACGCCTGAAAAAACAGGGCAATAAAGTCGAACTGTTGCCAGAAAACAGCGAg                                                             <  1:360863/69‑1 (MQ=255)
      gaCGAAGTTACCGTTAAACGCCTGAAAAAACAGGGCAATAAAGTCGAACTGTTGCCAGAAAACAGCGAg                                                             <  1:3083834/69‑1 (MQ=255)
      gaCGAAGTTACCGTTAAACGCCTGAAAAAACAGGGCAATAAAGTCGAACTGTTGCCAGAAAACAGCGAg                                                             <  1:1961648/69‑1 (MQ=255)
      gaCGAAGTTACCGTTAAACGCCTGAAAAAACAGGGCAATAAAGTCGAACTGTTGCCAGAAAACAGCGAg                                                             <  1:1995947/69‑1 (MQ=255)
      gaCGAAGTTACCGTTAAACGCCTGAAAAAACAGGGCAATAAAGTCGAACTGTTGCCAGAAAACAGCGAg                                                             <  1:2607888/69‑1 (MQ=255)
      gaCGAAGTTACCGTTAAACGCCTGAAAAAACAGGGCAATAAAGTCGAACTGTTGCCAGAAAACAGCGAg                                                             <  1:70101/69‑1 (MQ=255)
      gaCGAAGTTACCGTTAAACGCCTGAAAAAACAGGGCAATAAAGTCGAACTGTTGCCAGAAAACAGCGAg                                                             <  1:210564/69‑1 (MQ=255)
      gaCGAAGTTACCGTTAAACGCCTGAAAAAACAGGGCAATAAAGTCGAACTGTTGCCAGAAAACAGCGAg                                                             <  1:1113655/69‑1 (MQ=255)
      gaCGAAGTTACCGTTAAACGCCTGAAAAAACAGGGCAATAAAGTCGAACTGTTGCCAGAAAACAGCGAg                                                             <  1:1097187/69‑1 (MQ=255)
      gaCGAAGTTACCGTTAAACGCCTGAAAAAACAGGGCAATAAAGTCGAACTGTTGCCAGAAAACAGCGAg                                                             <  1:776858/69‑1 (MQ=255)
      gaCGAAGTTACCGTTAAACGCCTGAAAAAACAGGGCAATAAAGTCGAACTGTTGCCAGAAAACAGCGAg                                                             <  1:2173454/69‑1 (MQ=255)
       aCGAAGTTACCGTTAAACGCCTGAAAAAACAGGGCAATAAAGTCGAACTGTTGCCAGAAAACAGCGAg                                                             <  1:3302844/68‑1 (MQ=255)
       aCGAAGTTACCGTTAAACGCCTGAAAAAACAGGGCAATAAAGTCGAACTGTTGCCAGAAAACAGCGAg                                                             <  1:2984268/68‑1 (MQ=255)
       aCGAAGTTACCGTTAAACGCCTGAAAAAACAGGGCAATAAAGTCGAACTGTTGCCAGAAAACAGCGAg                                                             <  1:1038516/68‑1 (MQ=255)
          aaGTTACCGTTAAACGCCTGAAAAAACAGGGCAATAAAGTCGAACTGTTGCCAGAAAACAGCGAGTTTa                                                         <  1:1617970/69‑1 (MQ=255)
          aaGTTACCGTTAAACGCCTGAAAAAACAGGGCAATAAAGTCGAACTGTTGCCAGAAAACAGCGAGTTTa                                                         <  1:1568791/69‑1 (MQ=255)
          aaGTTACCGTTAAACGCCTGAAAAAACAGGGCAATAAAGTCGAACTGTTGCCAGAAAACAGCGAGTTTa                                                         <  1:368143/69‑1 (MQ=255)
          aaGTTACCGTTAAACGCCTGAAAAAACAGGGCAATAAAGTCGAACTGTTGCCAGAAAACAGCGAGTTTa                                                         <  1:1771601/69‑1 (MQ=255)
          aaGTTACCGTTAAACGCCTGAAAAAACAGGGCAATAAAGTCGAACTGTTGCCAGAAAACAGCGAGTTTa                                                         <  1:744946/69‑1 (MQ=255)
              tACCGTTAAGCGCCTGAAAAAACAGGGCAATAAAGTCGAACTGTTGCCAGAAAATAGCGAGTTTAAAcc                                                     >  1:3404312/1‑69 (MQ=255)
               aCCGTTAAGCGCCTGAAAAAACAGGGCAATAAAGTCGAACTGTTGCCAGAAAATAGCGAGTTTAAACCa                                                    >  1:1224821/1‑69 (MQ=255)
               aCCGTTAAGCGCCTGAAAAAACAGGGCAATAAAGTCGAACTGTTGCCAGAAAATAGCGAGTTTAAACCa                                                    >  1:957935/1‑69 (MQ=255)
                        cgcCTGAAAAAACAGGGCAATAAAGTCGAACTGTTGCCAGAAAACAg                                                                 >  1:686828/1‑47 (MQ=255)
                        cgcCTGAAAAAACAGGGCAATAAAGTCGAACTGTTGCCAGAAAACATCGAGTTTAAACCAAt                                                  >  1:580742/1‑62 (MQ=255)
                        cgcCTGAAAAAACAGGGCAATAAAGTCGAACTGTTGCCAGAAAACAGCGAGTTTAAACCAAt                                                  >  1:3055931/1‑62 (MQ=255)
                        cgcCTGAAAAAACAGGGCAATAAAGTCGAACTGTTGCCAGAAAACAGCGAGTTTAAACCAAt                                                  >  1:2514590/1‑62 (MQ=255)
                        cgcCTGAAAAAACAGGGCAATAAAGTCGAACTGTTGCCAGAAAACAGCGAGTTTAAACCAAt                                                  >  1:472133/1‑62 (MQ=255)
                        cgcCTGAAAAAACAGGGCAATAAAGTCGAACTGTTGCCAGAAAACAGCGAGTTTAAACCAAt                                                  >  1:639525/1‑62 (MQ=255)
                        cgcCTGAAAAAACAGGGCAATAAAGTCGAACTGTTGCCAGAAAACAGCGAGTTTAAACCAAt                                                  >  1:2518680/1‑62 (MQ=255)
                        cgcCTGAAAAAACAGGGCAATAAAGTCGAACTGTTGCCAGAAAACAGCGAGTTTAAACCAAt                                                  >  1:2241041/1‑62 (MQ=255)
                        cgcCTGAAAAAACAGGGCAATAAAGTCGAACTGTTGCCAGAAAACAGCGAGTTTAAACCAAt                                                  >  1:223879/1‑62 (MQ=255)
                        cgcCTGAAAAAACAGGGCAATAAAGTCGAACTGTTGCCAGAAAACAGCGAGTTTAAACCAAt                                                  >  1:1973224/1‑62 (MQ=255)
                        cgcCTGAAAAAACAGGGCAATAAAGTCGAACTGTTGCCAGAAAACAGCGAGTTTAAACCAAt                                                  >  1:1220863/1‑62 (MQ=255)
                        cgcCTGAAAAAACAGGGCAATAAAGTCGAACTGTTGCCAGAAAACAGCGAGTTTAAACCAAt                                                  >  1:1527857/1‑62 (MQ=255)
                        cgcCTGAAAAAACAGGGCAATAAAGTCGAACTGTTGCCAGAAAACAGCGAGTTTAAACCAAt                                                  >  1:1606995/1‑62 (MQ=255)
                        cgcATGAAAAAACAGGGCAATAAAGTCGAACTGTTGCCAGAAAACAGCGAGTTTAAAc                                                      >  1:3121242/1‑58 (MQ=39)
                         gcCTGAAAAAACAGGGCAATAAAGTCGAACTGTTGCCAGAAAATAGCGAGTTTAAACCAATTGTCGTTg                                          >  1:1361531/1‑69 (MQ=255)
                         gcCTGAAAAAACAGGGCAATAAAGTCGAACTGTTGCCAGAAAATAGCGAGTTTAAACCAATTGTCGTTg                                          >  1:2451209/1‑69 (MQ=255)
                         gcCTGAAAAAACAGGGCAATAAAGTCGAACTGTTGCCAGAAAATAGCGAGTTTAAACCAATTGTCGTTg                                          >  1:2544162/1‑69 (MQ=255)
                           cTGAAAAAACAGGGCAATAAAGTCGAACTGTTGCCAGAAAATAGCGAGTTTAAACCAATTGTCGTTGAc                                        <  1:2208804/69‑1 (MQ=255)
                           cTGAAAAAACAGGGCAATAAAGTCGAACTGTTGCCAGAAAATAGCGAGTTTAAACCAATTGTCGTTGAc                                        <  1:287430/69‑1 (MQ=255)
                           cTGAAAAAACAGGGCAATAAAGTCGAACTGTTGCCAGAAAATAGCGAGTTTAAACCAATTGTCGTTGAc                                        <  1:3048002/69‑1 (MQ=255)
                           cTGAAAAAACAGGGCAATAAAGTCGAACTGTTGCCAGAAAATAGCGAGTTTAAACCAATTGTCGTTGAc                                        <  1:1613607/69‑1 (MQ=255)
                           cTGAAAAAACAGGGCAATAAAGTCGAACTGTTGCCAGAAAATAGCGAGTTTAAACCAATTGTCGTTGAc                                        <  1:3411848/69‑1 (MQ=255)
                            tGAAAAAACAGGGCAATAAAGTCGAACTGTTGCCAGAAAATAGCGAGTTTAAACCAATTGTCGTTGAc                                        <  1:2491262/68‑1 (MQ=255)
                                aaaaCAGGGCAATAAAGTCGAACTGTTGCCAGAAAATAGCGAGTTTAAACCAATTGTCGTTGACCTTc                                    >  1:177785/1‑68 (MQ=255)
                                aaaaCAGGGCAATAAAGTCGAACTGTTGCCAGAAAATAGCGAGTTTAAACCAATTGTCGTTGACCTTc                                    >  1:1443470/1‑68 (MQ=255)
                                aaaaCAGGGCAATAAAGTCGAACTGTTGCCAGAAAATAGCGAGTTTAAACCAATTGTCGTTGACCTTc                                    >  1:965314/1‑68 (MQ=255)
                                aaaaCAGGGCAATAAAGTCGAACTGTTGCCAGAAAATAGCGAGTTTAAACCAATTGTCGTTGACCTTc                                    >  1:2748813/1‑68 (MQ=255)
                                aaaaCAGGGCAATAAAGTCGAACTGTTGCCAGAAAATAGCGAGTTTAAACCAATTGTCGTTGACCTTc                                    >  1:2375862/1‑68 (MQ=255)
                                aaaaCAGGGCAATAAAGTCGAACTGTTGCCAGAAAATAGCGAGTTTAAACCAATTGTCGTTGACCTTc                                    >  1:1027358/1‑68 (MQ=255)
                                   aCAGGGCAATAAAGTCGAACTGTTGCCAGAAAATAGCGAGTTTAAACCAATTGTCGTTGACCTTCGt                                  >  1:1774677/1‑67 (MQ=255)
                                   aCAGGGCAATAAAGTCGAACTGTTGCCAGAAAATAGCGAGTTTAAACCAATTGTCGTTGACCTTCGTc                                 >  1:2055174/1‑68 (MQ=255)
                                   aCAGGGCAATAAAGTCGAACTGTTGCCAGAAAATAGCGAGTTTAAACCAATTGTCGTTGACCTTCGTc                                 >  1:256561/1‑68 (MQ=255)
                                   aCAGGGCAATAAAGTCGAACTGTTGCCAGAAAATAGCGAGTTTAAACCAATTGTCGTTGACCTTCGTc                                 >  1:1624370/1‑68 (MQ=255)
                                   aCAGGGCAATAAAGTCGAACTGTTGCCAGAAAATAGCGAGTTTAAACCAATTGTCGTTGACCTTCGTc                                 >  1:3377327/1‑68 (MQ=255)
                                   aCAGGGCAATAAAGTCGAACTGTTGCCAGAAAATAGCGAGTTTAAACCAATTGTCGTTGACCTTCGTc                                 >  1:3220648/1‑68 (MQ=255)
                                    cAGGGCAATAAAGTCGAACTGTTGCCAGAAAATAGCGAGTTTAAACCAATTGTCGTTGACCTTCGTc                                 >  1:2186778/1‑67 (MQ=255)
                                    cAGGGCAATAAAGTCGAACTGTTGCCAGAAAATAGCGAGTTTAAACCAATTGTCGTTGACCTTCGTc                                 >  1:2057339/1‑67 (MQ=255)
                                    cAGGGCAATAAAGTCGAACTGTTGCCAGAAAATAGCGAGTTTAAACCAATTGTCGTTGACCTTCGTc                                 >  1:1676426/1‑67 (MQ=255)
                                    cAGGGCAATAAAGTCGAACTGTTGCCAGAAAATAGCGAGTTTAAACCAATTGTCGTTGACCTTCGTc                                 >  1:2529444/1‑67 (MQ=255)
                                       ggCAATAAAGTCGAACTGTTGCCAGAAAATAGCGAGTTTAAACCAATTGTCGTTGACCTTCGTcagcag                            >  1:2907608/1‑69 (MQ=255)
                                              aaGTCGAACTGTTGCCAGAAAATAGCGAGTTTAAACCAATTGTCGTTGACCTTCGTCAGCAGAGCTTc                      >  1:408489/1‑68 (MQ=255)
                                              aaGTCGAACTGTTGCCAGAAAATAGCGAGTTTAAACCAATTGTCGTTGACCTTCGTCAGCAGAGCTTc                      >  1:546291/1‑68 (MQ=255)
                                              aaGTCGAACTGTTGCCAGAAAATAGCGAGTTTAAACCAATTGTCGTTGACCTTCGTCAGCAGAGCTTc                      >  1:629781/1‑68 (MQ=255)
                                              aaGTCGAACTGTTGCCAGAAAATAGCGAGTTTAAACCAATTGTCGTTGACCTTCGTCAGCAGAGCTTc                      >  1:1672543/1‑68 (MQ=255)
                                              aaGTCGAACTGTTGCCAGAAAATAGCGAGTTTAAACCAATTGTCGTTGACCTTCGTCAGCAGAGCTTc                      >  1:2299085/1‑68 (MQ=255)
                                              aaGTCGAACTGTTGCCAGAAAATAGCGAGTTTAAACCAATTGTCGTTGACCTTCGTCAGCAGAGCTTc                      >  1:1297381/1‑68 (MQ=255)
                                              aaGTCGAACTGTTGCCAGAAAATAGCGAGTTTAAACCAATTGTCGTTGACCTTCGTCAGCAGAGCTTc                      >  1:1817480/1‑68 (MQ=255)
                                              aaGTCGAACTGTTGCCAGAAAATAGCGAGTTTAAACCAATTGTCGTTGACCTTCGTCAGCAGAGCTTc                      >  1:920500/1‑68 (MQ=255)
                                                gTCGAACTGTTGCCAGAAAATAGCGAGTTTAAACCAATTGTCGTTGACCTTCGTCAGCAGAGCTTCAc                    <  1:1281910/68‑1 (MQ=255)
                                                gTCGAACTGTTGCCAGAAAATAGCGAGTTTAAACCAATTGTCGTTGACCTTCGTCAGCAGAGCTTCAc                    <  1:1400906/68‑1 (MQ=255)
                                                gTCGAACTGTTGCCAGAAAATAGCGAGTTTAAACCAATTGTCGTTGACCTTCGTCAGCAGAGCTTCAc                    <  1:2711056/68‑1 (MQ=255)
                                                gTCGAACTGTTGCCAGAAAATAGCGAGTTTAAACCAATTGTCGTTGACCTTCGTCAGCAGAGCTTCAc                    <  1:2403659/68‑1 (MQ=255)
                                                gTCGAACTGTTGCCAGAAAATAGCGAGTTTAAACCAATTGTCGTTGACCTTCGTCAGCAGAGCTTCAc                    <  1:2746172/68‑1 (MQ=255)
                                                gTCGAACTGTTGCCAGAAAATAGCGAGTTTAAACCAATTGTCGTTGACCTTCGTCAGCAGAGCTTCAc                    <  1:2643979/68‑1 (MQ=255)
                                                gTCGAACTGTTGCCAGAAAATAGCGAGTTTAAACCAATTGTCGTTGACCTTCGTCAGCAGAGCTTCAc                    <  1:3186303/68‑1 (MQ=255)
                                                      cTGTTGCCAGAAAATAGCGAGTTTAAACCAATTGTCGTTGACCTTCGTCAGCAGAGCTTCACCATTGaa             >  1:1668373/1‑69 (MQ=255)
                                                      cTGTTGCCAGAAAATAGCGAGTTTAAACCAATTGTCGTTGACCTTCGTCAGCAGAGCTTCACCATTGaa             >  1:661051/1‑69 (MQ=255)
                                                      cTGTTGCCAGAAAATAGCGAGTTTAAACCAATTGTCGTTGACCTTCGTCAGCAGAGCTTCACCATTGaa             >  1:867442/1‑69 (MQ=255)
                                                        gTTGCCAGAAAATAGCGAGTTTAAACCAATTGTCGTTGACCTTCGTCAGCAGAGCTTCACCATTGAAgg           <  1:1289957/69‑1 (MQ=255)
                                                        gTTGCCAGAAAATAGCGAGTTTAAACCAATTGTCGTTGACCTTCGTCAGCAGAGCTTCACCATTGAAgg           <  1:1060352/69‑1 (MQ=255)
                                                        gTTGCCAGAAAATAGCGAGTTTAAACCAATTGTCGTTGACCTTCGTCAGCAGAGCTTCACCATTGAAgg           <  1:1050094/69‑1 (MQ=255)
                                                        gTTGCCAGAAAATAGCGAGTTTAAACCAATTGTCGTTGACCTTCGTCAGCAGAGCTTCACCATTGAAgg           <  1:1469561/69‑1 (MQ=255)
                                                           gCCAGAAAATAGCGAGTTTAAACCAATTGTCGTTGACCTTCGTCAGCAGAGCTTCACCATTGAAGGGCt        >  1:1811709/1‑69 (MQ=255)
                                                                 aaaTAGCGAGTTTAAACCAATTGTCGTTGACCTTCGTc                                 >  1:3424631/1‑38 (MQ=255)
                                                                 aaaTAGCGAGTTTAAACCAATTGTCGTTGACCTTCGTCAGCAGAGCTTCACCATTGAAGGGCTGGCGGt  >  1:57099/1‑69 (MQ=255)
                                                                 aaaTAGCGAGTTTAAACCAATTGTCGTTGACCTTCGTCAGCAGAGCTTCACCATTGAAGGGCTGGCGGt  >  1:2048713/1‑69 (MQ=255)
                                                                 aaaTAGCGAGTTTAAACCAATTGTCGTTGACCTTCGTCAGCAGAGCTTCACCATTGAAGGGCTGGCGGt  >  1:2502208/1‑69 (MQ=255)
                                                                 aaaTAGCGAGTTTAAACCAATTGTCGTTGACCTTCGTCAGCAGAGCTTCACCATTGAAGGGCTGGCGGt  >  1:2857166/1‑69 (MQ=255)
                                                                    |                                                                 
ATTGATGACGAAGTTACCGTTAAGCGCCTGAAAAAACAGGGCAATAAAGTCGAACTGTTGCCAGAAAATAGCGAGTTTAAACCAATTGTCGTTGACCTTCGTCAGCAGAGCTTCACCATTGAAGGGCTGGCGGT  >  minE/2796433‑2796566

Alignment Legend
Aligned base mismatch/match (shaded by quality score): ATCG/ATCG < 3 ≤ ATCG/ATCG < 27 ≤ ATCG/ATCG < 32 ≤ ATCG/ATCG < 36 ≤ ATCG/ATCG
Unaligned base: atcg    Masked matching base: atcg    Alignment gap: ‑    Deleted base: ‑

GATK/CNVnator alignment

N/A