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
A6 F1 I0 R1 2892 75.3 5698161 66.1% 3766484 59.5

Breseq alignment

BRESEQ :: Evidence
Predicted mutation
evidence seq id position mutation freq annotation gene description
RA minE 2,595,761 G→T 35.4% P279P (CCC→CCA)  arsB ← arsenite/antimonite transporter

Read alignment evidence...
  seq id position ref new freq score (cons/poly) reads annotation genes product
*minE2,595,7610GT35.4% 127.2 / 73.1 93P279P (CCC→CCA) arsBarsenite/antimonite transporter
Reads supporting (aligned to +/- strand):  ref base G (33/27);  new base T (17/16);  total (50/43)
Fisher's exact test for biased strand distribution p-value = 8.29e-01
Kolmogorov-Smirnov test that lower quality scores support variant p-value = 9.84e-01

Only 100 of 103 total aligned reads displayed.

CCGTTAATCCGGCATTGCGCAGGCCATAAACCACCAGATACATGCCGAGCGAGAAGATGACAATCTGCCAGGGGGCACCGCGCAGGACTTTACCCGTATTAATCGCATGACCGCGTTTAGCGACGACAAATAATATCAG  >  minE/2595691‑2595829
                                                                      |                                                                    
ccGTTAATCCGGCATTGCGCAGGCCATAAACCACCAGATACATGCCGAGCGAGAAGATGACAATCTGCCAg                                                                      >  1:3361955/1‑71 (MQ=255)
    tAATCCGGCATTGCGCAGGCCATAAACCACCAGATACATGCCGAGCGAGAAGATGACAATCTGCCAggggg                                                                  >  1:2040723/1‑71 (MQ=255)
     aaTCCGGCATTGCGCAGGCCATAAACCACCAGATACATGCCGAGCGAGAAGATGACAATCTGCCAggggg                                                                  <  1:1520409/70‑1 (MQ=255)
     aaTCCGGCATTGCGCAGGCCATAAACCACCAGATACATGCCGAGCGAGAAGATGACAATCTGCCAggggg                                                                  <  1:5190734/70‑1 (MQ=255)
       tCCGGCATTGCGCAGGCCATAAACCACCAGATACATGCCGAGCGAGAAGATGACAATCTGCCAGGGGGc                                                                 <  1:553044/69‑1 (MQ=255)
       tCCGGCATTGCGCAGGCCATAAACCACCAGATACATGCCGAGCGAGAAGATGACAATCTGCCAGGGGGc                                                                 <  1:177354/69‑1 (MQ=255)
       tCCGGCATTGCGCAGGCCATAAACCACCAGATACATGCCGAGCGAGAAGATGACAATCTGCCAGGGGGc                                                                 <  1:395201/69‑1 (MQ=255)
            cATTGCGCAGGCCATAGACCACGATGTACATGCCCAGTGAGAAAATAACGATCTGCCATGGCGCACcgcg                                                           <  1:4448805/70‑1 (MQ=255)
            cATTGCGCAGGCCATAGACCACGATGTACATGCCCAGTGAGAAAATAACGATCTGCCATGGCGCACcgcg                                                           >  1:1359999/1‑70 (MQ=255)
            cATTGCGCAGGCCATAGACCACGATGTACATGCCCAGTGAGAAAATAACGATCTGCCATGGCGCACcgcg                                                           >  1:311521/1‑70 (MQ=255)
            cATTGCGCAGGCCATAAACCACCAGATACATGCCGAGCGAGAAGATGACAATCTGCCAggg                                                                    >  1:1810563/1‑61 (MQ=255)
            cATTGCGCAGGCCATAAACCACCAGATACATGCCGAGCGAGAAGATGACAATCTGCCAGGGGGCACcgcg                                                           >  1:4283970/1‑70 (MQ=255)
            cATTGCGCAGGCCATAAACCACCAGATACATGCCGAGCGAGAAGATGACAATCTGCCAGGGGGCACcgcg                                                           >  1:5508891/1‑70 (MQ=255)
            cATTGCGCAGGCCATAAACCACCAGATACATGCCGAGCGAGAAGATGACAATCTGCCAGGGGGCACcgcg                                                           >  1:3923888/1‑70 (MQ=255)
              ttGCGCAGGCCATAGACCACGATGTACATGCCCAGTGAGAAAATAACGATCTGCCATGGCGCACCGCGCa                                                         >  1:1753101/1‑70 (MQ=255)
              ttGCGCAGGCCATAAACCACCAGATACATGCCGAGCGAGAAGATGACAATCTGCCAGGGGGCACCGCGCAg                                                        <  1:4337317/71‑1 (MQ=255)
               tGCGCAGGCCATAGACCACGATGTACATGCCCAGTGAGAAAATAACGATCTGCCATGGCGCACCGCGCAg                                                        >  1:4959400/1‑70 (MQ=255)
               tGCGCAGGCCATAGACCACGATGTACATGCCCAGTGAGAAAATAACGATCTGCCATGGCGCACCGCGCAg                                                        >  1:2682276/1‑70 (MQ=255)
                gcgcAGGCCATAGACCACGATGTACATGCCCAGTGAGAAAATAACGATCTGCCAtggc                                                                   >  1:4981360/1‑57 (MQ=255)
                gcgcAGGCCATAGACCACGATGTACATGCCCAGTGAGAAAATAACGATCTGCCAtggc                                                                   >  1:5300690/1‑57 (MQ=255)
                gcgcAGGCCATAGACCACGATGTACATGCCCAGTGAGAAAATAACGATCTGCCATGGCGCACCGCGCAgg                                                       <  1:1432804/70‑1 (MQ=255)
                gcgcAGGCCATAAACCACCAGATACATGCCGAGCGAGAAGATGACAATCTGCCAGGGGGCACCGCGCAGGa                                                      >  1:3144657/1‑71 (MQ=255)
                gcgcAGGCCATAAACCACCAGATACATGCCGAGCGAGAAGATGACAATCTGCCAGGGGGCACCGCGCAGGa                                                      >  1:5474520/1‑71 (MQ=255)
                 cgcAGGCCATAAACCACCAGATACATGCCGAGCGAGAAGATGACAATCTGCCAGGGGGCACCGCGCAGGAc                                                     <  1:3725958/71‑1 (MQ=255)
                   cAGGCCATAAACCACCAGATACATGCCGAGCGAGAAGATGACAATCTGCCAGGGGGCACCGCGCAGGACtt                                                   >  1:117966/1‑71 (MQ=255)
                    aGGCCATAGACCACGATGTACATGCCCAGTGAGAAAATAACGATCTGCCATGGCGCACCGCGCAGGACttt                                                  <  1:3163220/71‑1 (MQ=255)
                    aGGCCATAGACCACGATGTACATGCCCAGTGAGAAAATAACGATCTGCCATGGCGCACCGCGCAGGACtt                                                   <  1:5676939/70‑1 (MQ=255)
                     ggCCATAGACCACGATGTACATGCCCAGTGAGAAAATAACGATCTGCCATGGCGCACCGCGCAGGACtt                                                   <  1:2847733/69‑1 (MQ=255)
                      gCCATAAACCACCAGATACATGCCGAGCGAGAAGATGACAATCTGCCAGGGGGCACCGCGCAGGACTTTAc                                                >  1:3936944/1‑71 (MQ=255)
                       ccATAGACCACGATGTACATGCCCAGTGAGAAAATAACGATCTGCCATGGCGCACCGCGCAGGACtttt                                                 >  1:176605/1‑68 (MQ=255)
                       ccATAGACCACGATGTACATGCCCAGTGAGAAAATAACGATCTGCCATGGCGCACCGCGCAGGACtttt                                                 >  1:3117455/1‑68 (MQ=255)
                        cATAAACCACCAGATACATGCCGAGCGAGAAGATGACAATCTGCCAgg                                                                     >  1:1163787/1‑48 (MQ=255)
                         aTAGACCACGATGTACATGCCCAGTGAGAAAATAACGATCTGCCATGGCGCACCGCGCAGGAc                                                     <  1:3387899/63‑1 (MQ=255)
                         aTAGACCACGATGTACATGCCCAGTGAGAAAATAACGATCTGCCATGGCGCACCGCGCAGGAc                                                     <  1:192852/63‑1 (MQ=255)
                         aTAGACCACGATGTACATGCCCAGTGAGAAAATAACGATCTGCCATGGCGCACCGCGCAGGAc                                                     <  1:4301593/63‑1 (MQ=255)
                         aTAGACCACGATGTACATGCCCAGTGAGAAAATAACGATCTGCCATGGCGCACCGCGCAGGAc                                                     <  1:1097056/63‑1 (MQ=255)
                         aTAGACCACGATGTACATGCCCAGTGAGAAAATAACGATCTGCCATGGCGCACCGCGCAGGAc                                                     <  1:786349/63‑1 (MQ=255)
                         aTAGACCACGATGTACATGCCCAGTGAGAAAATAACGATCTGCCATGGCGCACCGCGCAGGACTTTTccgg                                             <  1:906572/71‑3 (MQ=255)
                         aTAAACCACCAGATACATGCCGAGCGAGAAGATGACAATCTGCCAg                                                                      >  1:5338130/1‑46 (MQ=255)
                          tAAACCACCAGATATATGCCGAGCGAGAAGATGACAATCTGCCAggggg                                                                  <  1:4049902/49‑1 (MQ=255)
                          tAAACCACCAGATACATGCCGAGCGAGAAGATGACAATCTGCCAGGGGGCACCGCGCAGGACTTTAccc                                              <  1:299542/69‑1 (MQ=255)
                            aaCCACCAGATACATGCCGAGCGAGAAGATGACAATCTGCCAGGGGGCAcc                                                              >  1:5229832/1‑51 (MQ=255)
                            aaCCACCAGATACATGCCGAGCGAGAAGATGACAATCTGCCAGGGGGCAcc                                                              >  1:1532783/1‑51 (MQ=255)
                             accaccAGATACATGCCGAGCGAGAAGATGACAATCTGCCAGGGGGCACCGCGCAGGACTTTACCCGTAtt                                         <  1:719264/71‑1 (MQ=255)
                               caccaGATACATGCCGAGCGAGAAGATGACAATCTGCCAGGGGGCACCGCGCAGGACTTTACCCGTATTaa                                       <  1:257140/71‑1 (MQ=255)
                                 ccaGATACATGCCGAGCGAGAAGATGACAATCTGCCAGGGGGCACCGCGCAGGACTTTACCCGTATTAATc                                     <  1:2879642/71‑1 (MQ=255)
                                  caGATACATGCCGAGCGAGAAGATGACAATCTGCCAGGGGGCACCGCGCAGGACTTTACCCGTATTAATCg                                    <  1:3722434/71‑1 (MQ=255)
                                   aGATACATGCCGAGCGAGAAGATGACAATCTGCCAGGGGGCACCGCGCAg                                                        >  1:1036405/1‑50 (MQ=255)
                                   aGATACATGCCGAGCGAGAAGATGACAATCTGCCAGGGGGCACCGCGCAg                                                        >  1:234510/1‑50 (MQ=255)
                                     aTACATGCCGAGCGAGAAGATGACAATCTGCCAGGGGGCACCGCGCAGGACTTTACCCGTATTaa                                       >  1:2385229/1‑65 (MQ=255)
                                     aTACATGCCGAGCGAGAAGATGACAATCTGCCAGGGGGCACCGCGCAGGACTTTACCCGTATTAATCGc                                   <  1:5510319/69‑1 (MQ=255)
                                     aTACATGCCGAGCGAGAAGATGACAATCTGCCAGGGGGCACCGCGCAGGACTTTACCCGTATTAATCGCAt                                 <  1:1668657/71‑1 (MQ=255)
                                      tACATGCCCAGTGAGAAAATAACGATCTGCCATGGCGCACCGCGCAGGACTTTTCCGGTGTTGATCGAAt                                 <  1:1845789/70‑1 (MQ=255)
                                       aCATGCCCAGTGAGAAAATAACGATCTGCCATGGCGCACCGCGCAGGACTTTTCCGGTGTTGATCGAATGa                               >  1:5107652/1‑71 (MQ=255)
                                        cATGCCCAGTGAGAAAATAACGATCTGCCATGGCGCACCGCGCAGGACTTTTCCGGtg                                           >  1:5689818/1‑57 (MQ=255)
                                        cATGCCCAGTGAGAAAATAACGATCTGCCATGGCGCACCGCGCAGGACTTTTCCGGtg                                           >  1:4378702/1‑57 (MQ=255)
                                        cATGCCCAGTGAGAAAATAACGATCTGCCATGGCGCACCGCGCAGGACTTTTCCGGTGTTGATCGAATGAc                              >  1:1060550/1‑71 (MQ=255)
                                        cATGCCCAGTGAGAAAATAACGATCTGCCATGGCGCACCGCGCAGGACTTTTCCGGTGTTGATCGAATGAc                              >  1:180481/1‑71 (MQ=255)
                                         aTGCCCAGTGAGAAAATAACGATCTGCCATGGCGCACCGCGCAGGAc                                                     <  1:2724969/47‑1 (MQ=255)
                                          tGCCGAGCGAGAAGATGACAATCTGCCAGGGGGCACCGCGCAGGACTTTACCCGTATTa                                        <  1:2975736/59‑1 (MQ=255)
                                          tGCCCAGTGAGAAAATAACGATCTGCCATGGCGCACCGCGCAGGACttt                                                  <  1:4840439/49‑1 (MQ=255)
                                          tGCCCAGTGAGAAAATAACGATCTGCCATGGCGCACCGCGCAGGACttt                                                  <  1:4282590/49‑1 (MQ=255)
                                           gCCGAGCGAGAAGATGACAATCTGCCAGGGGGCACCGCGCAGGa                                                      >  1:3895040/1‑44 (MQ=255)
                                           gCCGAGCGAGAAGATGACAATCTGCCAGGGGGCACCGCGCAGGa                                                      >  1:4394685/1‑44 (MQ=255)
                                            ccGAGCGAGAAGATGACAATCTGCCAGGGGGCACCGCGCAGGACTTTACCCGTATTAATCGCATGACcgcg                          <  1:2361138/71‑1 (MQ=255)
                                             cgagcgagAAGATGACAATCTGCCAGGGGGCACCGCGCAGGACTTTACCCGTATTAATCGCATGACCGCGt                         <  1:4160915/71‑1 (MQ=255)
                                               agcgagAAGATGACAATCTGCCAGGGGGCACCGCGCAGGACTTTACCCGTATTAATCGCATGACCGCGt                         >  1:1319482/1‑69 (MQ=255)
                                               agcgagAAGATGACAATCTGCCAGGGGGCACCGCGCAGGACTTTACCCGTATTAATCGCATGACCGCGt                         >  1:3451039/1‑69 (MQ=255)
                                                   agaaaaTAACGATCTGCCATGGCGCACCGCGCAGGACtt                                                   >  1:3309099/1‑39 (MQ=19)
                                                   agaaaaTAACGATCTGCCATGGCGCACCGCGCAGGACTTTTccg                                              >  1:1081720/1‑43 (MQ=255)
                                                    gaagaTGACAATCTTCCAGGGGGCACCGCGCAGGACTTTACCCGTATTAATCGCATGACCGCGtt                        >  1:5332342/1‑65 (MQ=255)
                                                    gaagaTGACAATCTGCCAGGGGGCACCGCGCAGGACTTTACCCGTATTAATCGCATGACCGCGtt                        >  1:189617/1‑65 (MQ=255)
                                                    gaagaTGACAATCTGCCAGGGGGCACCGCGCAGGACTTTACCCGTATTAATCGCATGACCGCGtt                        >  1:2317579/1‑65 (MQ=255)
                                                    gaagaTGACAATCTGCCAGGGGGCACCGCGCAGGACTTTACCCGTATTAATCGCATGACCGCGTTTAGcga                  >  1:713254/1‑71 (MQ=255)
                                                     aagaTGACAATCTGCCAGGGGGCACCGCGCAGGACTTTACCCGTATTAATCGCATGACcgc                           >  1:1017289/1‑61 (MQ=255)
                                                        aTGACAATCTGCCAGGGGGCACCGCGCAGGACTTTACCCGTATTa                                        <  1:4941705/45‑1 (MQ=255)
                                                        aTGACAATCTGCCAGGGGGCACCGCGCAGGACTTTACCCGTATTAATCGCATGACCGCGTTTAGcgacga               >  1:4151440/1‑70 (MQ=255)
                                                        aTGACAATCTGCCAGGGGGCACCGCGCAGGACTTTACCCGTATTAATCGCATGACCGCGTTTAGCgacgac              <  1:1089310/71‑1 (MQ=255)
                                                        aTGACAATCTGCCAGGGGGCACCGCGCAGGACTTTACCCGTATTAATCGCATGACCGCGTTTAGCgacgac              <  1:4033741/71‑1 (MQ=255)
                                                         tGACAATCTGCCAGGGGGCACCGCGCAGGACTTTACCCGTATTAATCGCATGa                               >  1:2307392/1‑53 (MQ=255)
                                                         tGACAATCTGCCAGGGGGCACCGCGCAGGACTTTACCCGTATTAATCGCATGa                               >  1:3044607/1‑53 (MQ=255)
                                                         tGACAATCTGCCAGGGGGCACCGCGCAGGACTTTACCCGTATTAATCGCATGACCGCGTTTAGCGACGACa             <  1:694332/71‑1 (MQ=255)
                                                          gACAATCTGCCAGGTGGCACCGCGCAGGACTTTACCCGTATTAATCGCATGACCGCGTTTAGc                    >  1:2381533/1‑63 (MQ=255)
                                                          gACAATCTGCCAGGGGGCACCGCGCAGGACTTTACCCGTATTAATCGCATGACCGCGTTTAGc                    >  1:2823252/1‑63 (MQ=255)
                                                          gACAATCTGCCAGGGGGCACCGCGCAGGACTTTACCCGTATTAATCGCATGACCGCGTTTAGc                    >  1:1600690/1‑63 (MQ=255)
                                                          gACAATCTGCCAGGGGGCACCGCGCAGGACTTTACCCGTATTAATCGCATGACCGCGTTTAGCGACGACa             >  1:1396365/1‑70 (MQ=255)
                                                           aCAATCTGCCAGGGGGCACCGCGCAGGACTTTACCCGTATTAATCGCATGACCGCGTTTAGCGACGACaaa           <  1:1027949/71‑1 (MQ=255)
                                                           aCAATCTGCCAGGGGGCACCGCGCAGGACTTTACCCGTATTAATCGCATGACCGCGTTTAGCGACGACaaa           <  1:4115735/71‑1 (MQ=255)
                                                            cAATCTGCCAGGGGGCACCGCGCAGGACTTTACCCGTATTAATCGCATGACCGCGTTTAGCGACGACaaa           >  1:2115101/1‑70 (MQ=255)
                                                            cAATCTGCCAGGGGGCACCGCGCAGGACTTTACCCGTATTAATCGCATGACCGCGTTTAGCGACGACAaat          <  1:3595832/71‑1 (MQ=255)
                                                              aTCTGCCAGGGGGCACCGCGCAGGACTTTACCCGTATTa                                        <  1:5520304/39‑1 (MQ=255)
                                                              aTCTGCCAGGGGGCACCGCGCAGGACTTTACCCGTATTAATCGCATGACCGCGt                         <  1:3955823/54‑1 (MQ=255)
                                                              aTCTGCCAGGGGGCACCGCGCAGGACTTTACCCGTATTAATCGCATGACCGCGTTTAGCGACGACAaataa        <  1:5658511/71‑1 (MQ=255)
                                                               tCTGCCATGGCGCACCGCGCAGGACTTTTCCGGTGTTGATCGAATGACCTCTTTTCGCCACCACaaacag        >  1:1109487/1‑67 (MQ=255)
                                                                cTGCCAGGGGGCACCGCGCAGGACTTTACCCGTATTAATCGCATGACCGCGTTTAGCGACGACaaa           >  1:3463228/1‑66 (MQ=255)
                                                                   ccATGGCGCACCGCGCAGGACTTTTCCGGTGTTGATCGAATGACCTCtttt                       >  1:334792/1‑51 (MQ=255)
                                                                   ccATGGCGCACCGCGCAGGACTTTTCCGGTGTTGATCGAATGACCTCTTTTCGCCACCACaaacag        <  1:3102050/66‑4 (MQ=255)
                                                                   ccAGGGGGCACCGCGCAGGACTTTACCCGTATTAATCGCATGACCGCGTTTAGCGACGACAaataat       <  1:5305533/67‑1 (MQ=255)
                                                                   ccAGGGGGCACCGCGCAGGACTTTACCCGTATTAATCGCATGACCGCGTTTAGCGACGACAAATAatat     <  1:5287046/69‑1 (MQ=255)
                                                                    cAGGGGGCACCGCGCAGGACTTTACCCGTATTAATCGCATGACCGCGTTTAGCGACGACAAATAATATCAg  >  1:4824907/1‑71 (MQ=255)
                                                                      |                                                                    
CCGTTAATCCGGCATTGCGCAGGCCATAAACCACCAGATACATGCCGAGCGAGAAGATGACAATCTGCCAGGGGGCACCGCGCAGGACTTTACCCGTATTAATCGCATGACCGCGTTTAGCGACGACAAATAATATCAG  >  minE/2595691‑2595829

Alignment Legend
Aligned base mismatch/match (shaded by quality score): ATCG/ATCG < 3 ≤ ATCG/ATCG < 14 ≤ ATCG/ATCG < 32 ≤ ATCG/ATCG < 36 ≤ ATCG/ATCG
Unaligned base: atcg    Masked matching base: atcg    Alignment gap: ‑    Deleted base: ‑

GATK/CNVnator alignment

N/A