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
A5 F17 I0 R1 87 56.5 4283937 98.6% 4223961 62.0

Breseq alignment

BRESEQ :: Evidence
Predicted mutation
evidence seq id position mutation freq annotation gene description
RA W3110S.gb 1,084,947 A→G 16.9% K384E (AAA→GAA)  ycdB → conserved hypothetical protein

Read alignment evidence...
  seq id position ref new freq score (cons/poly) reads annotation genes product
*W3110S.gb1,084,9470AG16.9% 139.6 / 21.7 59K384E (AAA→GAA) ycdBconserved hypothetical protein
Reads supporting (aligned to +/- strand):  ref base A (20/29);  new base G (6/4);  total (26/33)
Fisher's exact test for biased strand distribution p-value = 3.11e-01
Kolmogorov-Smirnov test that lower quality scores support variant p-value = 1.00e+00

AACTGGATATGGGGTTGCTGTTTGTCTGCTACCAACACGATCTGGAAAAAGGCTTCCTGACAGTACAAAAAAGGCTCAATGGCGAAGCGCTGGAGGAATACGTTAAACCTATCGGCGGCGGTTATTTTTTTGCGCTGCC  >  W3110S.gb/1084879‑1085017
                                                                    |                                                                      
aaCTGGATATGGGGTTGCTGTTTGTCTGCTACCAACACGATCTGGAAAAAGGCTTCCTGACAGTACaaaaa                                                                      <  1:2429300/71‑1 (MQ=255)
    ggATATGGGGTTGCTGTTTGTCTGCTACCAACACGATCTGGAAAAAGGCTTCCTGACAGTACAAAAAAGGc                                                                  >  1:708025/1‑71 (MQ=255)
     gATATGGGGTTGCTGTTTGTCTGCTACCAACACGATCTGGAAAAAGGCTTCCTGACAGTACAAAAAAGGc                                                                  <  1:969523/70‑1 (MQ=255)
      atatGGGGTTGCTGTTTGTCTGCTACCAACACGATCTGGAAAAAGGCTTCCTGACAGTACAAAAAAGGCTc                                                                <  1:1180173/71‑1 (MQ=255)
            ggTTGCTGTTTGTCTGCTACCAACACGATCTGGAAAAAGGCTTCCTGACAGTACAAAAAAGGCTCAATGGc                                                          <  1:498264/71‑1 (MQ=255)
             gTTGCTGTTTGTCTGCTACCAACACGATCTGGAAAAAGGCTTCCTGACAGTACAAAAAAGGCTCaa                                                              <  1:2505808/66‑1 (MQ=255)
             gTTGCTGTTTGTCTGCTACCAACACGATCTGGAAAAAGGCTTCCTGACAGTACAAAAAAGGCTCaa                                                              <  1:2646418/66‑1 (MQ=255)
             gTTGCTGTTTGTCTGCTACCAACACGATCTGGAAAAAGGCTTCCTGACAGTACAAAAAAGGCTCAATGGCg                                                         <  1:1819309/71‑1 (MQ=255)
               tgatGTTTGTCTGCTACCAACACGATCTGGAAAAAGGCTTCCTGACAGTACAAAAAAGGCTCAATg                                                            >  1:4035577/4‑66 (MQ=255)
               tGCTGTTTGTCTGCTACCAACACGATCTGGAAAAAGGCTTCCTGACAGTACAAAAAAGGCTCAATGGCg                                                         >  1:2827408/1‑69 (MQ=255)
               tGCTGTTTGTCTGCTACCAACACGATCTGGAAAAAGGCTTCCTGACAGTACAAAAAAGGCTCAATGGCg                                                         >  1:2090131/1‑69 (MQ=255)
                gCTGTTTGTCTGCTACCAACACGATCTGGAAAAAGGCTTCCTGACAGTACaaaaaa                                                                     >  1:1774455/1‑56 (MQ=255)
                gCTGTTTGTCTGCTACCAACACGATCTGGAAAAAGGCTTCCTGACAGTACaaaaaa                                                                     >  1:1779562/1‑56 (MQ=255)
                gCTGTTTGTCTGCTACCAACACGATCTGGAAAAAGGCTTCCTGACAGTACaaaaaa                                                                     >  1:2886831/1‑56 (MQ=255)
                gCTGTTTGTCTGCTACCAACACGATCTGGAAAAAGGCTTCCTGACAGTACAAAAAAGGCTCAATGGCGaa                                                       <  1:762084/70‑1 (MQ=255)
                gCTGTTTGTCTGCTACCAACACGATCTGGAAAAAGGCTTCCTGACAGTACAAAAAAGGCT‑AATGGc                                                          >  1:1210350/1‑66 (MQ=255)
                    tttGTCTGCTACCAACACGATCTGGAAAAAGGCTTCCTGACAGTACAAAAAAGGCTCAATGGCGAAGCGCt                                                  >  1:1789121/1‑71 (MQ=255)
                    tttGTCTGCTACCAACACGATCTGGAAAAAGGCTTCCTGACAGTACAAAAAAGGCTCAATGGCGAAGCGCt                                                  >  1:2897463/1‑71 (MQ=255)
                     ttGTCTGCTACCGACACGATCTGGAAAAAGGCTTCCTGACAGTACAAAAAAGGCTCAATGGCGaa                                                       >  1:1486470/1‑65 (MQ=255)
                     ttGTCTGCTACCAACACGATCTGGAAAAAGGCTTCCTGACAGTACAAAAAAGGCTCAATGGCGaa                                                       >  1:1803510/1‑65 (MQ=255)
                      tGTCTGCTACCAACACGATCTGGAAAAAGGCTTCCTGACAGTACAAGAAAGGCTCAATGGCGAAGCGCTg                                                 <  1:1555741/70‑1 (MQ=255)
                          tGCTACCAACACGATCTGGAAAAAGGCTTCCTGACAGTACAAAAAAGGCTCAATGGc                                                          <  1:1971133/57‑1 (MQ=255)
                            cTACCAACACGATCTGGAAAAAGGCTTCCTGACAGTACAAAAAAGGCTCAATGGCGAAgc                                                     >  1:3457980/1‑60 (MQ=255)
                            cTACCAACACGATCTGGAAAAAGGCTTCCTGACAGTACAAAAAAGGCTCAATGGCGAAGCGCTttagga                                            <  1:4207611/69‑1 (MQ=255)
                            cTACCAACACGATCTGGAAAAAGGCGTCCTGACAGTACAAAAAAGGCTCAATGGCGAAGCGCTGGAGGAAt                                          <  1:1541518/71‑1 (MQ=255)
                             tACCAACACGATCTGGAAAAAGGCTTCCTGACAGTACAAAAAAGGCt                                                                 <  1:1042637/47‑1 (MQ=255)
                              aCCAACACGATCTGGAAAAAGGCTTCCTGACAGTACaaaa                                                                       >  1:446545/1‑40 (MQ=255)
                              aCCAACACGATCTGGAAAAAGGCTTCCTGACAGTACAAAAAAGGCTCAATGGCGAAGCGCTGGAGGaa                                           >  1:4165415/1‑68 (MQ=255)
                               ccAACACGATCTGGAAAAAGGCTTCCTGACAGTACaaaaaa                                                                     >  1:640258/1‑41 (MQ=255)
                               ccAACACGATCTGGAAAAAGGCTTCCTGACAGTACAAGAAAGGCTCAATGGCGAAGCGCTGGAGGAATACg                                       >  1:1335644/1‑71 (MQ=255)
                               ccAACACGATCTGGAAAAAGGCTTCCTGACAGTACAAAAAAGGCTCAATGGCGAAGCGCTGGAGGAATACg                                       >  1:202982/1‑71 (MQ=255)
                                cAACACGATCTGGAAAAAGGCTTCCTGACAGTACAAGAAAGGCTCAATGGCGAAGCGCTGGAGGAATACGt                                      >  1:190739/1‑71 (MQ=255)
                                cAACACGATCTGGAAAAAGGCTTCCTGACAGTACAAAAAAGGCTc                                                                <  1:2273124/45‑1 (MQ=255)
                                   cacGATCTGGAAAAAGGCTTCCTGACAGTACaaaaaa                                                                     <  1:294994/37‑1 (MQ=255)
                                   cacGATCTGGAAAAAGGCTTCCTGACAGTACAAGGAAGGCTCAATGGCGAAGCGCTGGAGGAATACGTTa                                    >  1:4231811/1‑70 (MQ=255)
                                   cacGATCTGGAAAAAGGCTTCCTGACAGTACAAAAAAGGCTCAATGGCGAAGCGCTGGAGGAATACGt                                      <  1:3674586/68‑1 (MQ=255)
                                   cacGATCTGGAAAAAGGCTTCCTGACAGTACAAAAAAGGCTCAATGGCGAAGCGCTGGAGGAATACGTTaa                                   <  1:2724572/71‑1 (MQ=255)
                                    acGATCTGGAAAAAGGCTTCCTGACAGTACaaaaaa                                                                     >  1:1105783/1‑36 (MQ=255)
                                    acGATCTGGAAAAAGGCTTCCTGACAGTACAAGAAAGGCTCAATGGCGAAGCGCTGGAGGAATACGTTaaa                                  <  1:2011136/71‑1 (MQ=255)
                                    acGATCTGGAAAAAGGCTTCCTGACAGTACAAGAAAGGCTCAATGGCGAAGCGCTGGAGGAATACGTTaaa                                  <  1:1190643/71‑1 (MQ=255)
                                     cGATCTGGAAAAAGGCTTCCTGACAGTACAAAAAAGGCTCAATGGCGAAGCGCTGGAGGAATACGTTAAAc                                 >  1:3407872/1‑71 (MQ=255)
                                      gATCTGGAAAAAGGCTTCCTGACAGTACAAAAAAGGCTCAATGGCGAAGCGCTGGAGGAATACGTTAAAcc                                >  1:3332862/1‑71 (MQ=255)
                                       aTCTGGAAAAAGGCTTCCTGACAGTACAAAAAAGGCTCAATGGCGa                                                        <  1:1804393/46‑1 (MQ=255)
                                        tCTGGAAAAAGGCTTCCTGACAGTACAAGAAAGGCTCAATGGCGAAg                                                      >  1:2325717/1‑47 (MQ=255)
                                         cTGGAAAAAGGCTTCCTGACAGTACAAAAAAGGCTCAATGGCGaa                                                       >  1:156993/1‑45 (MQ=255)
                                         cTGGAAAAAGGCTTCCTGACAGTACAAAAAAGGCTCAATGGCGAAGCGCTGGAGGAATACGTTAAACCTAt                             >  1:2230243/1‑71 (MQ=255)
                                          tGGAAAAAGGCTTCCTGACAGTACAAAAAAGGCTCAATGGCGAAGCGCt                                                  <  1:934509/49‑1 (MQ=255)
                                          tGGAAAAAGGCTTCCTGACAGTACAAAAAAGGCTCAATGGCGAAGCGCTgg                                                <  1:824035/51‑1 (MQ=255)
                                          tGGAAAAAGGCTTCCTGACAGTACAAAAAAGGCTCAATGGCGAAGCGCTGGAGGAAt                                          <  1:3317073/57‑1 (MQ=255)
                                           ggAAAAAGGCTTCCTGACAGTACAAAAAAGGCTCAATGGCGAAGCGCTGGAGGAATa                                         >  1:1388329/1‑57 (MQ=255)
                                            gAAAAAGGCTTCCTGACAGTACAAAAAAGGCTCAATGGCGAAGCGCTGGAGGAATACGTTAAAcc                                <  1:1060417/65‑1 (MQ=255)
                                            gAAAAAGGCTTCCTGACAGTACAAAAAAGGCTCAATGGCGAAGCGCTGGAGGAATACGTTAAACCt                               <  1:1169359/66‑1 (MQ=255)
                                              aaaaGGCTTCCTGACAGTACAAAAAAGGCTCAATGGCGAAGCGCTggagga                                            >  1:1449481/1‑51 (MQ=255)
                                              aaaaGGCTTCCTGACAGTACAAAAAAGGCTCAATGGCGAAGCGCTggagg                                             >  1:3159351/1‑50 (MQ=255)
                                              aaaaGGCTTCCTGACAGTACAAAAAAGGCTCAATGGCGAAGCGCTGGAGGAATa                                         >  1:861465/1‑54 (MQ=255)
                                                   gCTTCCTGACAGTACAAAAAAGGCTCAATGGCGAAGCGCTGGAGGAATACGTTAAACCt                               <  1:3275570/59‑1 (MQ=255)
                                                       ccTGACAGTACAAGAAAGGCTCAATGGCGAAGCGCTGGAGGAATACGTTAAACCTATCGGCGGCGGTTAtt               >  1:313517/1‑71 (MQ=255)
                                                       ccTGACAGTACAAAAAAGGCTCAATGGCGAAGCGCTGGAGGAATACGTTAAATCTATCGGCGGCGGtt                  <  1:1822954/68‑1 (MQ=255)
                                                       ccTGACAGTACAAAAAAGGCTCAATGGCGAAGCGCTGGAGGAATACGTTAAACCTATCGGCGGCGGTTAt                <  1:2860992/70‑1 (MQ=255)
                                                          gACAGTACAAAAAAGGCTCAATGGCGAAGCGCTGGAGGAATACGt                                      <  1:1681563/45‑1 (MQ=255)
                                                           aCAGTACAAGAAAGGCTCAATGGCGAAGCGCTGGAGGAATACGTTAAACCTATCGGCGGCGGTTAttttt            <  1:235429/70‑1 (MQ=255)
                                                           aCAGTACAAAAAAGGCTCAATGGCGAAGCGCTGGAGGAATACGTTAAACCTATCGGCGGCGGTTAttttt            <  1:1223905/70‑1 (MQ=255)
                                                             aGTACAAGAAAGGCTCAATGGCGAAGCGCTGGAGGAATACGTTAAACCTATCGGCGGCGGTTa                 >  1:761174/1‑63 (MQ=255)
                                                              gTACAAAAAAGGCTCAATGGCGAAGCGCTGGAGGAATACGTTAAACCTATCGGCGGCGGTTATTTTTTTg         <  1:3247018/70‑1 (MQ=255)
                                                               tACAAAAAAGGCTCAATGGCGAAGCGCTTGAGGAATACGTTAAACCTATcg                           <  1:1974200/51‑1 (MQ=255)
                                                                aCAAAAAAGGCTCAATGGCGAAGCGCTGGAGGAATACGTTAAACCTATCGGCGGCGGTTAttttt            <  1:3350851/65‑1 (MQ=255)
                                                                 cAAAAAAGGCTCAATGGCGAAGCGCTGGAGGAATa                                         <  1:3951432/35‑1 (MQ=255)
                                                                    aaaaGGCTCAATGGCGAAGCGCTGGAGGAATACGTTAAACCTa                              >  1:345151/1‑43 (MQ=255)
                                                                    aaaaGGCTCAATGGCGAAGCGCTGGAGGAATACGTTAAACCTATCGGCGGCGGTTATTTTTTTGCGCTGcc  >  1:2432841/1‑71 (MQ=255)
                                                                    |                                                                      
AACTGGATATGGGGTTGCTGTTTGTCTGCTACCAACACGATCTGGAAAAAGGCTTCCTGACAGTACAAAAAAGGCTCAATGGCGAAGCGCTGGAGGAATACGTTAAACCTATCGGCGGCGGTTATTTTTTTGCGCTGCC  >  W3110S.gb/1084879‑1085017

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