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 F3 I0 R2 232 76.3 4135488 90.9% 3759158 60.7

Breseq alignment

BRESEQ :: Evidence
Predicted mutation
evidence seq id position mutation freq annotation gene description
RA minE 2,321,698 G→A 22.8% T93I (ACC→ATC)  cdh ← CDP‑diacylglycerol phosphotidylhydrolase

Read alignment evidence...
  seq id position ref new freq score (cons/poly) reads annotation genes product
*minE2,321,6980GA22.8% 236.0 / 67.2 114T93I (ACC→ATC) cdhCDP‑diacylglycerol phosphotidylhydrolase
Reads supporting (aligned to +/- strand):  ref base G (39/49);  new base A (18/8);  total (57/57)
Fisher's exact test for biased strand distribution p-value = 4.33e-02
Kolmogorov-Smirnov test that lower quality scores support variant p-value = 5.58e-01

Only 100 of 115 total aligned reads displayed.

GTATTTTTTGCTCATAAAATCACGCGCCTGCCAAGCCAACCAAAAGAAGTTCGGCGTTGAAGGATCGGTCAACAAAGGACTTTCAGTACCGTTAATACGATACGTTGGCATCAACAGATATTGCAGTGGGCCATT  >  minE/2321631‑2321765
                                                                   |                                                                   
gTATTTTTTGCTCATAAAATCACGCGCCTGCCAAGCCAACCAAAAGAAGTTCGGCGTTGAAGGATCGGTc                                                                   >  1:2417292/1‑70 (MQ=255)
gTATTTTTTGCTCATAAAATCACGCGCCTGCCAAGCCAACCAAAAGAAGTTCGGCGTTGAAGGATCGGTc                                                                   >  1:2240684/1‑70 (MQ=255)
   ttttttGCTCATAAAATCACGCGCCTGCCAAGCCACCCAAAAGAAGTTCGGCGTTGAAGGATCGGTcaac                                                                >  1:3323338/1‑70 (MQ=255)
   ttttttGCTCATAAAATCACGCGCCTGCCAAGCCAACCAAAAGAAGTTCGGCGTTGAAGGATCGGTcaac                                                                <  1:3472785/70‑1 (MQ=255)
     ttttGCTCATAAAATCACGCGCCTGCCAAGCCAACCAAAAGAAGTTCGGCGTTGAAGGATCGGTcaaca                                                               >  1:1990566/1‑69 (MQ=255)
          cTCATAAAATCACGCGCCTGCCAAGCCAACCAAAAGAAGTTCGGCGTTGAAGGATCGGTCAACAAAGGACt                                                        >  1:1072313/1‑71 (MQ=255)
          cTCATAAAATCACGCGCCTGCCAAGCCAACCAAAAGAAGTTCGGCGTTGAAGGATCGGTCAACAAAGGACt                                                        >  1:2105815/1‑71 (MQ=255)
          cTCATAAAATCACGCGCCTGCCAAGCCAACCAAAAGAAGTTCGGCGTTGAAGGATCGGTCAACAAAGGACt                                                        >  1:3201883/1‑71 (MQ=255)
          cTCATAAAATCACGCGCCTGCCAAGCCAACCAAAAGAAGTTCGGCGTTGAAGGATCGGTCAACAAAGGACt                                                        >  1:634875/1‑71 (MQ=255)
            cATAAAATCACGCGCCTGCCAAGCCAACCAAAAGAAGTTCGGCGTTGAAGGATCGGTCAACAAAGGACttt                                                      >  1:3841725/1‑71 (MQ=255)
             aTAAAATCACGCGCCTGCCAAGCCAACCAAAAGAAGTTCGGCGTTGAAGGATCGGTCAACAAAGGACtt                                                       <  1:1998809/69‑1 (MQ=255)
              tAAAATCACGCGCCTGCCAAGCCAACCAAAAGAAGTTCGGCGTTGAAGGATCGGTCAACAAAGGACTTTc                                                     <  1:109124/70‑1 (MQ=255)
                aaaTCACGCGCCTGCCAAGCCAACCAAAAGAAGTTCGGCGTTGAAGGATCGGTCAACAAAGGACTTTCAg                                                   >  1:2681105/1‑70 (MQ=255)
                      cgcgCCTGCCAAGCCAACCAAAAGAAGTTCGGCGTTGAAGGATCGGTCAACAAAGGACTTTCAGTACCGtt                                            <  1:1942634/71‑1 (MQ=255)
                      cgcgCCTGCCAAGCCAACCAAAAGAAGTTCGGCGTTGAAGGATCGGTCAACAAAGGACTTTCAGTACCGtt                                            <  1:1017082/71‑1 (MQ=255)
                      cgcgCCTGCCAAGCCAACCAAAAGAAGTTCGGCGTTGAAGGATCGGTCAACAAAGGACTTTCAGTACCGtt                                            <  1:1346321/71‑1 (MQ=255)
                      cgcgCCTGCCAAGCCAACCAAAAGAAGTTCGGCGTTGAAGGATCGATCAACAAAGGACTTTCAGTACCGtt                                            <  1:1081283/71‑1 (MQ=255)
                      cgcgCCTGCCAAGCCAACCAAAAGAAGTTCGGCGTTGAAGGATCGATCAACAAAGGACTTTCAGTACCGtt                                            <  1:370920/71‑1 (MQ=255)
                       gcgcCTGCCAAGCCAACCAAAAGAAGTTCGGCGTTGAAGGATCGGTCAACAAAGGACTTTCAGTACCGtt                                            <  1:1639701/70‑1 (MQ=255)
                              ccaagccaaCCAAAAGAAGTTCGGCGTTGAAGGATCGGTCAACAAAGGACTTTCAGTACCGTTAatacga                                     >  1:210179/1‑70 (MQ=255)
                              ccaagccaaCCAAAAGAAGTTCGGCGTTGAAGGATCGGTCAACAAAGGACTTTCAGTACCGTTAatacga                                     >  1:3267777/1‑70 (MQ=255)
                              ccaagccaaCCAAAAGAAGTTCGGCGTTGAAGGATCGGTCAACAAAGGACTTTCAGTACCGTTAatacga                                     >  1:974643/1‑70 (MQ=255)
                              ccaagccaaCCAAAAGAAGTTCGGCGTTGAAGGATCGGTCAACAAAGGACTTTCAGTACCGTTAatacga                                     >  1:2709372/1‑70 (MQ=255)
                              ccaagccaaCCAAAAGAAGTTCGGCGTTGAAGGATCGGTCAACAAAGGACTTTAAGTACCGTTAatacga                                     >  1:3603882/1‑70 (MQ=255)
                               caagccaaCCAAAAGAAGTTCGGCGTTGAAGGATCGGTCAACAAAGGACTTTCAGTACCGTTAatac                                       >  1:1777898/1‑67 (MQ=255)
                                 agccaaCCAAAAGAAGTTCGGCGTTGAAGGATCGGTCAACAAAGGACTTTCAGTACCGt                                             <  1:575097/59‑1 (MQ=255)
                                 agccaaCCAAAAGAAGTTCGGCGTTGAAGGATCGGTCAACAAAGGACTTTCAGTACCGt                                             <  1:2786556/59‑1 (MQ=255)
                                 agccaaCCAAAAGAAGTTCGGCGTTGAAGGATCGGTCAACAAAGGACTTTCAGTACCGTTAatacgatacg                                 <  1:924086/71‑1 (MQ=255)
                                   ccaaccaaAAGAAGTTCGGCGTTGAAGGATCGGTCAACAAAGGACTTTCAGTACCGTTa                                           >  1:2905071/1‑59 (MQ=255)
                                   ccaaccaaAAGAAGTTCGGCGTTGAAGGATCGGTCAACAAAGGACTTTCAGTACCGTTa                                           >  1:1896771/1‑59 (MQ=255)
                                   ccaaccaaAAGAAGTTCGGCGTTGAAGGATCGGTCAACAAAGGACTTTCAGTACCGTTa                                           >  1:2909951/1‑59 (MQ=255)
                                     aaccaaAAGAAGTTCGGCGTTGAAGGATCGGTCAACAAAGGACttt                                                      <  1:2187765/46‑1 (MQ=255)
                                     aaccaaAAGAAGTTCGGCGTTGAAGGATCGGTCAACAAAGGACttt                                                      <  1:3119412/46‑1 (MQ=255)
                                        caaAAGAAGTTCGGCGTTGAAGGATCGGTCAACAAAGGa                                                          >  1:1436599/1‑39 (MQ=255)
                                        caaAAGAAGTTCGGCGTTGAAGGATCGGTCAACAAAGGACTTTCAGTACCGTTaa                                          >  1:461730/1‑55 (MQ=255)
                                        caaAAGAAGTTCGGCGTTGAAGGATCGGTCAACAAAGGACTTTCAGTACCGTTAatacga                                     >  1:13662/1‑60 (MQ=255)
                                         aaaaGAAGTTCGGCGTTGAAGGATCGGTCAACAAAGGACTTTCAGTACCGTTAATACGATACGTTGGCATc                         <  1:2207219/71‑1 (MQ=255)
                                         aaaaGAAGTTCGGCGTTGAAGGATCGATCAACAAAg                                                            >  1:1361521/1‑36 (MQ=255)
                                         aaaaGAAGTTCGGCGTTGAAGGATCGATCAACAAAg                                                            >  1:1152731/1‑36 (MQ=255)
                                         aaaaGAAGTTCGGCGTTGAAGGATCGATCAACAAAg                                                            >  1:1079049/1‑36 (MQ=255)
                                         aaaaGAAGTTCGGCGTTGAAGGATCGATCAACAAAg                                                            >  1:346028/1‑36 (MQ=255)
                                         aaaaGAAGTTCGGCGTTGAAGGATCGATCAACAAAg                                                            >  1:1474691/1‑36 (MQ=255)
                                          aaaGAAGTTCGGCGTTGAAGGATCGGTCAACAAAGGACTTTCAGTACCGTTAATACGATACGTTGGCATc                         <  1:2677370/70‑1 (MQ=255)
                                            agaagTTCGGCGTTGAAGGATCGGTCAACAAAGGAc                                                         >  1:3529818/1‑36 (MQ=255)
                                            agaagTTCGGCGTTGAAGGATCGGTCAACAAAGGACTTTCAGTACCGTTAATACGATACGTTGGCATCaa                       >  1:1500599/1‑70 (MQ=255)
                                            agaagTTCGGCGTTGAAGGATCGGTCAACAAAGGACTTTCAGTACCGTTAATACGATACGTTGGCATCaa                       >  1:3534681/1‑70 (MQ=255)
                                            agaagTTCGGCGTTGAAGGATCGGTCAACAAAGGACTTTCAGTACCGTTAATACGATACGTTGGCATCaa                       >  1:709273/1‑70 (MQ=255)
                                              aagTTCGGCGTTGAAGGATCGGTCAACAAAGGACTTTCAGTACCGTTAATACGATACGTTGGCATCAACAg                    <  1:165027/71‑1 (MQ=255)
                                              aagTTCGGCGTTGAAGGATCGGTCAACAAAGGACTTTCAGTACCGTTAATACGATACGTTGGCATCAACAg                    <  1:2389734/71‑1 (MQ=255)
                                                gTTCGGCGTTGAAGGATCGGTCAACAAAGGACTTTCAGTACCGTTAATACGATACGTTGGCATCAACAGat                  <  1:719021/71‑1 (MQ=255)
                                                gTTCGGCGTTGAAGGATCGGTCAACAAAGGACTTTCAGTACCGTTAATACGATACGTTGGCATCAACAGat                  <  1:3575040/71‑1 (MQ=255)
                                                gTTCGGCGTTGAAGGATCGGTCAACAAAGGACTTTCAGTACCGTTAATACGATACGTTGGCATCAACAGat                  <  1:2035957/71‑1 (MQ=255)
                                                gTTCGGCGTTGAAGGATCGGTCAACAAAGGACTTTCAGTACCGTTAATACGATACGTTGGCATCAACAGat                  <  1:369587/71‑1 (MQ=255)
                                                gTTCGGCGTTGAAGGATCGGTCAACAAAGGACTTTCAGTACCGTTAATACGATACGTTGGCATCAACAGat                  <  1:1814101/71‑1 (MQ=255)
                                                gTTCGGCGTTGAAGGATCGGTCAACAAAGGACTTTCAGTACCGTTAATACGATACGTTGGCATCAACAGa                   <  1:2507049/70‑1 (MQ=255)
                                                 ttCGGCGTTGAAGGATCGATCAACAAAGGACTTTCAGTACCGtt                                            <  1:3916870/44‑1 (MQ=255)
                                                   cGGCGTTGAAGGATCGGTCAACAAAGGACTTTCAGTACCGTTAATACGATACGTTGGCATCAACAGATAtt               >  1:1285259/1‑71 (MQ=255)
                                                   cGGCGTTGAAGGATCGGTCAACAAAGGACTTTCAGTACCGTTAATACGATACGTTGGCATCAACAGATAtt               >  1:3937505/1‑71 (MQ=255)
                                                   cGGCGTTGAAGGATCGATCAACAAAGGACTTTCAGTACCGTTaa                                          >  1:2992943/1‑44 (MQ=255)
                                                   cGGCGTTGAAGGATCGATCAACAAAGGACTTTCAGTACCGTTaa                                          >  1:2988222/1‑44 (MQ=255)
                                                   cGGCGTTGAAGGATCGATCAACAAAGGACTTTCAGTACCGTTaa                                          >  1:3201499/1‑44 (MQ=255)
                                                   cGGCGTTGAAGGATCGATCAACAAAGGACTTTCAGTACCGTTAATACGATACGTTGGCATCAACAGatat                <  1:1908570/70‑1 (MQ=255)
                                                   cGGCGTTGAAGGATCGATCAACAAAGGACTTTCAGTACCGTTAATACGATACGTTGGCATCAACAGatat                >  1:2226151/1‑70 (MQ=255)
                                                   cGGCGTTGAAGGATCGATCAACAAAGGACTTTCAGTACCGTTAATACGATACGTTGGCATCAACAGatat                <  1:2289292/70‑1 (MQ=255)
                                                   cGGCGTTGAAGGATCGATCAACAAAGGACTTTCAGTACCGTTAATACGATACGTTGGCATCAACAGata                 >  1:981391/1‑69 (MQ=255)
                                                   cGGCGTTGAAGGATCGATCAACAAAGGACTTTCAGTACCGTTAATACGATACGTTGGCATCAACAGata                 >  1:3629554/1‑69 (MQ=255)
                                                   cGGCGTTGAAGGATCGATCAACAAAGGACTTTCAGTACCGTTAATACGATACGTTGGCATCAACAGata                 >  1:3872580/1‑69 (MQ=255)
                                                   cGGCGTTGAAGGATCGATCAACAAAGGACTTTCAGTACCGTTAATACGATACGTTGGCATCAACAGata                 >  1:1290881/1‑69 (MQ=255)
                                                   cGGCGTTGAAGGATCGATCAACAAAGGACTTTCAGTACCGTTAATACGATACGTTGGCATCAACAGata                 >  1:2653938/1‑69 (MQ=255)
                                                   cGGCGTTGAAGGATCGATCAACAAAGGACTTTCAGTACCGTTAATACGATACGTTGGCATCAACAGATAtt               >  1:3180337/1‑71 (MQ=255)
                                                    ggCGTTGAAGGATCGGTCAACAAAGGACTTTCAGTACCGTTAATACGATACGTTGGCATCAACAGatat                <  1:44250/69‑1 (MQ=255)
                                                    ggCGTTGAAGGATCGGTCAACAAAGGACTTTCAGTACCGTTAATACGATACGTTGGCATCAACAGATATTg              <  1:3377342/71‑1 (MQ=255)
                                                    ggCGTTGAAGGATCGGTCAACAAAGGACTTTCAGTACCGTTAATACGATACGTTGGCATCAACAGATATTg              <  1:2164715/71‑1 (MQ=255)
                                                    ggCGTTGAAGGATCGGTCAACAAAGGACTTTCAGTACCGTTAATACGATACGTTGGCATCAACAGATATTg              <  1:900989/71‑1 (MQ=255)
                                                     gCGTTGAAGGATCGGTCAACAAAGGACTTTCAGTACCGTTAATACGATACGTTGGCATCAACAGATATTGc             <  1:3164238/71‑1 (MQ=255)
                                                     gCGTTGAAGGATCGGTCAACAAAGGACTTTCAGTACCGTTAATACGATACGTTGGCATCAACAGATATTGc             <  1:3726898/71‑1 (MQ=255)
                                                     gCGTTGAAGGATCGGTCAACAAAGGACTTTCAGTACCGTTAATACGATACGTTGGCATCAACAGATATTGc             <  1:2218725/71‑1 (MQ=255)
                                                       gTTGAAGGATCGGTCAACAAAGGACTTTCAGTACCGTTAATACGATACGTTGGCATCAACAGATATTGCAg           <  1:1826972/71‑1 (MQ=255)
                                                        ttGAAGGATCGGTCAACAAAGGACTTTCAGTACCGtt                                            <  1:61791/37‑1 (MQ=255)
                                                        ttGAAGGATCGGTCAACAAAGGACTTTCAGTACCGTTAATACGATACGTTGGCATCAACa                     <  1:952165/60‑1 (MQ=255)
                                                        ttGAAGGATCGGTCAACAAAGGACTTTCAGTACCGTTAATACGATACGTTGGCATCAACa                     <  1:322440/60‑1 (MQ=255)
                                                          gAAGGATCGGTCAACAAAGGACTTTCAGTACCGtt                                            <  1:3610489/35‑1 (MQ=255)
                                                          gAAGGATCGGTCAACAAAGGACTTTCAGTACCGtt                                            <  1:2089552/35‑1 (MQ=255)
                                                          gAAGGATCGGTCAACAAAGGACTTTCAGTACCGTTAATACGATACGTTGGCATCAACAGat                  >  1:3365599/1‑61 (MQ=255)
                                                          gAAGGATCGGTCAACAAAGGACTTTCAGTACCGTTAATACGATACGTTGGCATCAACAGat                  >  1:3274154/1‑61 (MQ=255)
                                                          gAAGGATCGGTCAACAAAGGACTTTCAGTACCGTTAATACGATACGTTGGCATCAACAGat                  >  1:3038854/1‑61 (MQ=255)
                                                          gAAGGATCGATCAACAAAGGACTTTCAGTACCGTTAATACGATACGTTGGCATCAACAGATATTGCAGTgg        >  1:3315764/1‑71 (MQ=255)
                                                           aaGGATCGGTCAACAAAGGACTTTCAGTACCGTTAATACGATACGTTGGCATCAACAGat                  <  1:2494510/60‑1 (MQ=255)
                                                           aaGGATCGGTCAACAAAGGACTTTCAGTACCGTTAATACGATACGTTGGCATCAACAGat                  <  1:2546440/60‑1 (MQ=255)
                                                           aaGGATCGGTCAACAAAGGACTTTCAGTACCGTTAATACGATACGTTGGCATCAACAGat                  <  1:2641888/60‑1 (MQ=255)
                                                           aaGGATCGGTCAACAAAGGACTTTCAGTACCGTTAATACGATACGTTGGCATCAACAGat                  <  1:3488022/60‑1 (MQ=255)
                                                            aGGATCGGTCAACAAAGGACTTTCAGTACCGTTAATACGATACGTTGGCATCAACAGat                  <  1:209146/59‑1 (MQ=255)
                                                            aGGATCGGTCAACAAAGGACTTTCAGTACCGTTAATACGATACGTTGGCATCAACAGATATTGCAGTGGGc      >  1:1234220/1‑71 (MQ=255)
                                                                tCGGTCAACAAAGGACTTTCAGTACCGTTAATACGATACGTTGGCATCAACAGata                 >  1:1355125/1‑56 (MQ=255)
                                                                tCGGTCAACAAAGGACTTTCAGTACCGTTAATACGATACGTTGGCATCAACAGata                 >  1:94964/1‑56 (MQ=255)
                                                                tCGGTCAACAAAGGACTTTCAGTACCGTTAATACGATACGTTGGCATCAACAGATATTGCAGTGGGCCAtt  <  1:243120/71‑1 (MQ=255)
                                                                tCGGTCAACAAAGGACTTTCAGTACCGTTAATACGATACGTTGGCATCAACAGATATTGCAGTGGGCCAtt  <  1:162054/71‑1 (MQ=255)
                                                                tCGATCAACAAAGGACTTTCAGTACCGTTAATACGATACGTTGGCATCAACAGATATTGCAGTGGGCCAtt  <  1:2627583/71‑1 (MQ=255)
                                                                tCGATCAACAAAGGACTTTCAGTACCGTTAATACGATACGTTGGCATCAACAGATATTGCAGTGGGCCAt   >  1:116043/1‑70 (MQ=255)
                                                                  ggTCAACAAAGGACTTTCAGTACCGTTAATACGATACGTTGGCATCAACAGata                 >  1:2480910/1‑54 (MQ=255)
                                                                   |                                                                   
GTATTTTTTGCTCATAAAATCACGCGCCTGCCAAGCCAACCAAAAGAAGTTCGGCGTTGAAGGATCGGTCAACAAAGGACTTTCAGTACCGTTAATACGATACGTTGGCATCAACAGATATTGCAGTGGGCCATT  >  minE/2321631‑2321765

Alignment Legend
Aligned base mismatch/match (shaded by quality score): ATCG/ATCG < 3 ≤ ATCG/ATCG < 21 ≤ ATCG/ATCG < 32 ≤ ATCG/ATCG < 36 ≤ ATCG/ATCG
Unaligned base: atcg    Masked matching base: atcg    Alignment gap: ‑    Deleted base: ‑

GATK/CNVnator alignment

N/A