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 F21 I0 R1 2169 63.0 3952800 76.2% 3012033 62.4

Breseq alignment

BRESEQ :: Evidence
Predicted mutation
evidence seq id position mutation freq annotation gene description
RA minE 1,300,414 A→G 30.6% I237I (ATT→ATC)  yeeA ← conserved inner membrane protein

Read alignment evidence...
  seq id position ref new freq score (cons/poly) reads annotation genes product
*minE1,300,4140AG30.6% 73.1 / 48.0 62I237I (ATT→ATC) yeeAconserved inner membrane protein
Reads supporting (aligned to +/- strand):  ref base A (18/25);  new base G (11/8);  total (29/33)
Fisher's exact test for biased strand distribution p-value = 2.80e-01
Kolmogorov-Smirnov test that lower quality scores support variant p-value = 4.02e-01

CGAAATGGCTGGGGCGCGTGGCCCAGTATGCATTGATTTGCAACTCCAGCATACAAACCAGATTGCGGTTAATGGTCTGGATACCTTCATATATCGATTTTGGAATACGGGTTTCTTTGCTGGCGGGCGCAATCAGTC  >  minE/1300344‑1300481
                                                                      |                                                                   
cGAAATGGCTGGGGCGCGTGGCCCAGTATGCATTGATTTGCAACTCCAGCATACAAACCAGATTGCGGTTa                                                                     <  1:3555272/71‑1 (MQ=255)
     tGGCTGGGGCGCGTGGCCCAGTATGCATTGATTTGCAACTCCAGCATACAAACCAGATTGCGGTTAATGGt                                                                <  1:1164000/71‑1 (MQ=255)
     tGGCTGGGGCGCGTGGCCCAGTATGCATTGATTTGCAACTCCAGCATACAAACCAGATTGCGGTTAATGGt                                                                <  1:266440/71‑1 (MQ=255)
       gCTGGGGCGCGTGGCCCAGTATGCATTGATTTGCAACTCCAGCATACAAACCAGATTGCGGTTGATGGTCt                                                              <  1:287015/71‑1 (MQ=255)
       gCTGGGGCGCGTGGCCCAGTATGCATTGATTTGCAACTCCAGCATACAAACCAGATTGCGGTTAATGGTc                                                               <  1:1933990/70‑1 (MQ=255)
        cTGGGGCGCGTGGCCCAGTATGCATTGATTTGCAACTCCAGCATACAAACCAGATTGCGGTTAATGGTCTg                                                             <  1:331271/71‑1 (MQ=255)
             gcgcGTGGCCCAGTATGCATTGATTTGCAACTCCAGCATACAAACCAGATTGCGGTTAAt                                                                   <  1:2491434/60‑1 (MQ=255)
               gcgTGGCCCAGTATGCATTGATTTGCAACTCCAGCATACAAACCAGATTGCGGTTGATGGTCTGGATACCt                                                      >  1:97159/1‑71 (MQ=255)
               gcgTGGCCCAGTATGCATTGATTTGCAACTCCAGCATACAAACCAGATTGCGGTTAATGGTCTGGATACCt                                                      <  1:3541236/71‑1 (MQ=255)
               gcgTGGCCCAGTATGCATTGATTTGCAACTCCAGCATACAAACCAAATTGCGGTTAATGGTCTGGATACCt                                                      <  1:1032729/71‑1 (MQ=255)
                cgTGTCCCAGTATGCATTGATTTGCAACTCCAGCATACAAACCAGATTGCGGTTAATGGTCTg                                                             <  1:1227837/63‑1 (MQ=255)
                cgTGGCCCAGTATGCATTGATTTGCAACTCCAGCATACAAACCAGATTGCGGTTAATGGTCTg                                                             <  1:1994502/63‑1 (MQ=255)
                cgTGGCCCAGTATGCATTGATTTGCAACTCCAGCATACAAACCAGATTGCGGTTAATGGTCTGGATACCt                                                      <  1:3427283/70‑1 (MQ=255)
                 ggggCCCAGTATGCATTGATTTGCAACTCCAGCATACAAAACAGATTGCGGTTAATGGTCTGGATACCTTc                                                    <  1:1821874/69‑1 (MQ=255)
                  tGGCCCAGTATGCATTGATTTGCAACTCCAGCATACAAACCAGATTGCGGTTAATGGTCTGGATACCTTc                                                    <  1:3702444/70‑1 (MQ=255)
                     cccAGTATGCATTGATTTGCAACTCCAGCATACAAACCAGATTGCGGTTGATGGTCTGGATACCTTCatat                                                <  1:1238913/71‑1 (MQ=255)
                     cccAGTATGCATTGATTTGCAACTCCAGCATACAAACCAGATTGCGGTTAATGGTCTGGATACCTTCatat                                                <  1:67291/71‑1 (MQ=255)
                       cAGTATGCATTGATTTGCAACTCCAGCATACAAACCAGATTGCGGTTGATGGTCTGGATAcc                                                       >  1:2641009/1‑62 (MQ=255)
                       cAGTATGCATTGATTTGCAACTCCAGCATACAAACCAGATTGCGGTTGATGGTCTGGATACCTTCatatat                                              >  1:2269693/1‑71 (MQ=255)
                        aGTATGCATTGATTTGCAACTCCAGCATACAAACCAGATTGCGGTTGATGGTCTGGATACCTTCATATATc                                             <  1:1869066/71‑1 (MQ=255)
                        aGTATGCATTGATTTGCAACTCCAGCATACAAACCAGATTGCGGTTGATGGTCTGGATACCTTCATATATc                                             >  1:25736/1‑71 (MQ=255)
                         gTATGCATTGATTTGCAACTCCAGCATACAAACCAGATTGCGGTTAATGGTCTgg                                                            <  1:3747031/55‑1 (MQ=255)
                         gTATGCATTGATTTGCAACTCCAGCATACAAACCAGATTGCGGTTAATGGTCTgg                                                            <  1:1121115/55‑1 (MQ=255)
                              cATTGATTTGCAACTCCAGCATACAAACCAGATTGCGGTTAATGGTCTGGATACCTTCATATATCGAtttt                                       >  1:2482752/1‑71 (MQ=255)
                              cATTGATTTGCAACTCCAGCATACAAACCAGATTGCGGTTAATGGTCTGGATACCTTCATATATCGAtttt                                       >  1:1018563/1‑71 (MQ=255)
                              cATTGATTTGCAACTCCAGCATACAAACCAGATTGCGGTTAATGGTCTGGATACCTTCATATATCGAttt                                        <  1:2576475/70‑1 (MQ=255)
                              cATTGATTTGCAACTCCAGCATACAAACCAGATTGCGGTTAATGGTCTGGATACCTTCATATATCGAttt                                        <  1:3033549/70‑1 (MQ=255)
                               aTTGATTTGCAACTCCAGCATACAAACCAGATTGCGGTTAATGGTCTGGATACCTTc                                                    <  1:3143188/57‑1 (MQ=255)
                                ttGATTTGCAACTCCAGCATACAAACCAGATTGCGGTTAATGGTCTg                                                             >  1:2376466/1‑47 (MQ=255)
                                ttGATTTGCAACTCCAGCATACAAACCAGATTGCGGTTAATGGTCTGGATACCTTCata                                                 <  1:164107/59‑1 (MQ=255)
                                  gATTTGCAACTCCAGCATACAAACCAGATTGCGGTTGATGGt                                                                >  1:1720202/1‑42 (MQ=255)
                                  gATTTGCAACTCCAGCATACAAACCAGATTGCGGTTAATGGTCTGGATACCTTCATATATCGATTTTGGaa                                   >  1:3840982/1‑71 (MQ=255)
                                   aTTTGCAACTCCAGCATACAAACCAGATTGCGGTTAATGGt                                                                >  1:3457231/1‑41 (MQ=255)
                                     ttGCAACTCCAGCATACAAACCAGATTGCGGTTGATGGTCTGGATACCTTCATATATCGATTTTGGAATAc                                >  1:1242706/1‑71 (MQ=255)
                                      tGCAACTCCAGCATACAAACCAGATTGCGGTTGATGGTCTGGATAcc                                                       >  1:2699493/1‑47 (MQ=255)
                                      tGCAACTCCAGCATACAAACCAGATTGCGGTTGATGGTCTGGATACCTTCATATATCGATTTTGGAATAc                                <  1:3871556/70‑1 (MQ=255)
                                      tGCAACTCCAGCATACAAACCAGATTGCGGTTAATGGTCTGGATACCTTCATATATCGATTTTGGAATACg                               >  1:2649966/1‑71 (MQ=255)
                                      tGCAACTCCAGCATACAAA‑CAGATTGCGGTTGATGGTCTGGATAcc                                                       >  1:2031727/1‑46 (MQ=255)
                                          aCTCCAGCATACAAACCAGATTGCGGTTGATGGTCTGGATACCTTCATATATCGATTTTGGAATACGGGtt                           <  1:3262664/71‑1 (MQ=255)
                                           cTCCAGCATACAAACCAGATTGCGGTTAATGGTCTGGATACCTTCATATATCGATTTTGGAATACGGGttt                          <  1:980233/71‑1 (MQ=255)
                                           cTCCAGCATACAAACCAGATTGCGGTTAATGGTCTGGATACCTTCATATATCGATTTTGGAATACGGGttt                          <  1:2644002/71‑1 (MQ=255)
                                           cTCCAGCATACAAACCAGATTGCGGTTAATGGTCTGGATACCTTCATATATCGATTTTGGAATACGGGttt                          <  1:2226310/71‑1 (MQ=255)
                                            tCCAGCATACAAACCAGATTGCGGTTAATGGTCTGGATACCTTCATATATCGATTTTGGAATACGGGt                            <  1:1989298/68‑1 (MQ=255)
                                             ccAGCATACAAACCAGATTGCGGTTAATGGTCTGGATACCTTCATATATCGATTTTGGAATACgg                              >  1:997025/1‑65 (MQ=255)
                                              cAGCATAAAAACCAGATTGCGGTTAATGGTCTGGATACCTTCATATATCGATTTTGGAATACGGGTTTCtt                       >  1:1957796/1‑71 (MQ=255)
                                                 cATACAAACCAGATTGCGGTTGATGGTCTGGATACCTTCATATATCGATTTTGGAATACGGGTTTCttt                      >  1:1701708/1‑69 (MQ=255)
                                                  aTACAAACCAGATTGCGGTTGATGGTCTGGATACCTTCATATATCGATTTTGGAATACGGGTTTCTTTGc                    <  1:1335540/70‑1 (MQ=255)
                                                  aTACAAACCAGATTGCGGTTGATGGTCTGGATACCTTCATATATCGATTTTGGAATACGGGTTTCTTTGc                    <  1:1330989/70‑1 (MQ=255)
                                                  aTACAAACCAGATTGCGGTTAATGGTCTGGATACCTTCATATATCGATTTTGGAATACGGGTTTCTTTGCt                   >  1:2451819/1‑71 (MQ=255)
                                                   tACAAACCAGATTGCGGTTGATGGTCTGGATACCTTCATATATCGAttta                                       >  1:3218227/1‑49 (MQ=255)
                                                    aCAAACCAGATTGCGGTTGATGGTCTGGATACCTTCATATATCGATTTTGGAATACGGGTTTCTTTGCTgg                 >  1:3287072/1‑71 (MQ=255)
                                                     cAAACCAGATTGCGGTTAATGGTCTGGATACCTTCat                                                  >  1:2585029/1‑37 (MQ=255)
                                                      aaaCCAGATTGCGGTTAATGGTCTGGATACCTTCat                                                  >  1:2080523/1‑36 (MQ=255)
                                                      aaaCCAGATTGCGGTTAATGGTCTGGATACCTTCat                                                  >  1:2423537/1‑36 (MQ=255)
                                                      aaaCCAGATTGCGGTTAATGGTCTGGATACCTTCATATATCGATTTTGGAATACGGGTTTCTTTGCTggcg               <  1:61498/71‑1 (MQ=255)
                                                        aCCAGATTGCGGTTAATGGTCTGGATACCTTCATATATCGATTTTGGAATACgg                              >  1:1688174/1‑54 (MQ=255)
                                                          cAGATTGCGGTTAATGGTCTGGATACCTTCATATATCGATTTTGGAATACGGGTTTCTTTGCTgg                 >  1:1997488/1‑65 (MQ=255)
                                                           aGATTGCGGTTAATGGTCTGCATACCTTCATATATCGATTTTGGAATACGGGTTTCTTTGCTggcggg             >  1:1748617/1‑68 (MQ=255)
                                                            gATTGCGGTTAATGGTCTGGATACCTTCATATATCGATTTTGGAATACGGGTTTCTTTGCTggcgggcg           >  1:603364/1‑69 (MQ=255)
                                                              ttGCGGTTGATGGTCTGGATACCTTCATATATCGATTTTGGAATACGGGTTTCTTTGCTGGCGGGCGCAAt       <  1:1561183/71‑1 (MQ=255)
                                                                    ttAATGGTCTGGATACCTTCATATATCGATTTTGGaa                                   >  1:680511/1‑37 (MQ=255)
                                                                    ttAATGGTCTGGATACCTTCATATATCGATTTTGGAATACGGGTTTCTTTGCTGGCGGGCGCAAt       <  1:3055311/65‑1 (MQ=255)
                                                                    ttAATGGTCTGGATACCTTCATATATCGATTTTGGAATACGGGTTTCTTTGCTGGCGGGCGCAATCAGTc  >  1:3683304/1‑70 (MQ=255)
                                                                      aaTGGTCTGGATACCTTCATATATCGATTTTGGAATACg                               >  1:1771426/1‑39 (MQ=255)
                                                                      aaTGGTCTGGATACCTTCATATATCGATTTTGGAATACg                               >  1:1580051/1‑39 (MQ=255)
                                                                      |                                                                   
CGAAATGGCTGGGGCGCGTGGCCCAGTATGCATTGATTTGCAACTCCAGCATACAAACCAGATTGCGGTTAATGGTCTGGATACCTTCATATATCGATTTTGGAATACGGGTTTCTTTGCTGGCGGGCGCAATCAGTC  >  minE/1300344‑1300481

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