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
A1 F3 I0 R1 560 56.4 4650532 94.9% 4413354 59.3

Breseq alignment

BRESEQ :: Evidence
Predicted mutation
evidence seq id position mutation freq annotation gene description
RA W3110S.gb 2,213,335 A→G 19.7% N301S (AAT→AGT)  yehQ → hypothetical protein

Read alignment evidence...
  seq id position ref new freq score (cons/poly) reads annotation genes product
*W3110S.gb2,213,3350AG19.7% 130.4 / 27.1 61N301S (AAT→AGT) yehQhypothetical protein
Reads supporting (aligned to +/- strand):  ref base A (33/16);  new base G (6/6);  total (39/22)
Fisher's exact test for biased strand distribution p-value = 3.22e-01
Kolmogorov-Smirnov test that lower quality scores support variant p-value = 1.00e+00

CCCGCGCCAGCCACTATAATGCCGGAGAATGCTTACATCAGCTTGCGGCATTAAACAGTCGATTAAATTGCGCACAAGAGATGGCCCGGCGCGACAGTATTGGTGAAGTTCCTCCTGTGCCGTGGCGCACGGTCGT  >  W3110S.gb/2213269‑2213404
                                                                  |                                                                     
cccGCGCCAGCCACTATAATGCCGGAGAATGCTTACATCAGCTTGCGGCATTAAACAGTCGATTAAATTgc                                                                   >  1:3733151/1‑71 (MQ=255)
cccGCGCCAGCCACTATAATGCCGGAGAATGCTTACATCAGCTTGCGGCATTAAACAGTCGATTAAATTgc                                                                   >  1:1215198/1‑71 (MQ=255)
 ccGCGCCAGCCACTATAATGCCGGAGAATGCTTACATCAGCTTGCGGCATTAAACAGTCGATTAAATTgcg                                                                  <  1:1413204/71‑1 (MQ=255)
        agccaCTATAATGCCGGAGAATGCTTACATCAGCTTGCGGCATTAAACAGTCGATTAAATTGCGCACAaga                                                           <  1:3870103/71‑1 (MQ=255)
        agccaCTATAATGCCGGAGAATGCTTACATCAGCTTGCGGCATTAAACAGTCGATTAAATTGCGCACAaga                                                           <  1:3126238/71‑1 (MQ=255)
        agccaCTATAATGCCGGAGAATGCTTACATCAGCTTGCGGCATTAAACAGTCGATTAAATTGCGCACAaga                                                           <  1:31230/71‑1 (MQ=255)
          ccaCTATAATGCCGGAGAATGCTTACATCAGCTTGCGGCATTAAACAGTCGATTaaa                                                                       >  1:547697/1‑57 (MQ=255)
             cTATAATGCCGGAGAATGCTTACATCAGCTTGCGGCATTAAACAGTCGATTaaa                                                                       >  1:329831/1‑54 (MQ=255)
             cTATAATGCCGGAGAATGCTTACATCAGCTTGCGGCATTAAACAGTCGATTaaa                                                                       >  1:1299312/1‑54 (MQ=255)
             cTATAATGCCGGAGAATGCTTACATCAGCTTGCGGCATTAAACAGTCGATTAAATTGCGCACAAGAGATgg                                                      >  1:149242/1‑71 (MQ=255)
              tataATGCCGGAGAATGCTTACATCAGCTTGGGGCATTAAACAGTCGATTAAATTGCGCACAaga                                                           <  1:3764807/65‑1 (MQ=255)
               ataATGCCGGAGAATGCTTACATCAGCTTGCGGCATTAAACAGTCGATTAAATTGCGCACAAGAGATGGcc                                                    >  1:2036624/1‑71 (MQ=255)
                 aaTGCCGGAGAATGCTTACATCAGCTTGCGGCATTAAACAGTCGATTAAATTGCGCACAAGAGATGGCCCg                                                  >  1:2784035/1‑71 (MQ=255)
                  aTGCCGGAGAATGCTTACATCAGCTTGCGGCATTAAACAGTCGATTAAATTGCGCACAAGAGATGGCCCg                                                  >  1:2351087/1‑70 (MQ=255)
                  aTGCCGGAGAATGCTTACATCAGCTTGCGGCATTAAACAGTCGATTAAATTGCGCACAAGAGATGGCCCg                                                  >  1:2130628/1‑70 (MQ=255)
                     ccGGAGAATGCTTACATCAGCTTGCGGCATTAAACAGTCGATTAAGTTGCGCACAAGAGATGGTCCGgcgc                                              >  1:2634893/1‑71 (MQ=255)
                     ccGGAGAATGCTTACATCAGCTTGCGGCATTAAACAGTCGATTAAATTGCGCACAAGAGATGGCCCGgcgc                                              <  1:3606164/71‑1 (MQ=255)
                     ccGGAGAATGCTTACATCAGCTTGCGGCATTAAACAGTCGATTAAATTGCGCACAAGAGATGGCCCGgcgc                                              <  1:1700004/71‑1 (MQ=255)
                     ccGGAGAATGCTTACATCAGCTTGCGGCATTAAACAGTCGATTAAATTGCGCACAAGAGATGGCCCGgcgc                                              >  1:1228312/1‑71 (MQ=255)
                        gagaATGCTTACATCAGCTTGCGGCATTAAACAGTCGATTAAATTGCGCACAAGAGATGGCCCGGcgcg                                             <  1:1513449/69‑1 (MQ=255)
                          gaATGCTTACATCAGCTTGCGGCATTAAACAGTCGATTAAATTGCGCACAAGAGATGGCCCGGCGCGACAg                                         >  1:1884664/1‑71 (MQ=255)
                          gaATGCTTACATCAGCTTGCGGCATTAAACAGTCGATTAAATTGCGCACAAGAGATGGCCCGGCGCGACAg                                         <  1:1326185/71‑1 (MQ=255)
                          gaATGCTTACATCAGCTTGCGGCATTAAACAGTCGATTAAATTGCGCACAAGAGATGGCCCGGCGCGACAg                                         >  1:3871237/1‑71 (MQ=255)
                          gaATGCTTACATCAGCTTGCGGCATTAAACAGTCGATTAAATTGCGCACAAGAGATGGCCCGGCGCGACAg                                         <  1:4080469/71‑1 (MQ=255)
                          gaATGCTTACATCAGCTTCCGGCATTAAACAGTCGATTAAGTTGCGAACAAGAGATGGCCCgg                                                 >  1:1128968/1‑63 (MQ=255)
                           aaTGCTTACATCAGCTTGCGGCATTAAACAGTCGATTAAATTGCGCACAAGAGATg                                                       <  1:3440678/56‑1 (MQ=255)
                            aTGCTTACATCAGCTTGCGGCATTAAACAGTCGATTAAGTTgcg                                                                  <  1:4443301/44‑1 (MQ=255)
                             tGCTTACATCAGCTTGCGGCATTAAACAGTCGATTAAATTGCGCACAAGAGATGGCCCGGCGCGACAGTAt                                      >  1:4443515/1‑71 (MQ=255)
                             tGCTTACATCAGCTTGCGGCATTAAACAGTCGATTAAATTGCGCACAAGAGATGGCCCGGCGCGACAGTAt                                      >  1:1180926/1‑71 (MQ=255)
                             tGCTTACATCAGCTTGCGGCATTAAACAGTCGATTAAATTGCGCACAAGAGATGGCCCGGCGCGACAGTAt                                      >  1:2959423/1‑71 (MQ=255)
                             tGCTTACATCAGCTTGCGGCATTAAACAGTCGATTAAATTGCGCACAACAGATGGCCCGGCGCGa                                            >  1:1193581/1‑65 (MQ=255)
                               cTTACATCAGCTTGCGGCATTAAACAGTCGATTAAAtt                                                                     >  1:3934636/1‑38 (MQ=255)
                               cTTACATCAGCTTGCGGCATTAAACAGTCGATTAAATTGCGCACaa                                                             >  1:1000240/1‑46 (MQ=255)
                               cTTACATCAGCTTGCGGCATTAAACAGTCGATTAAATTGCGCACAAGAGATGGCCCGGCGCGACAGTATTg                                    >  1:553941/1‑71 (MQ=255)
                               cTTACATCAGCTTGCGGCATTAAACAGACGATTAAAta                                                                     >  1:604500/1‑37 (MQ=38)
                                ttACATCAGCTTGCGGCATTAAACAGTCGATTAAGTTCCGcac                                                               <  1:957144/43‑1 (MQ=38)
                                      cAGCTTGCGGCATTAAACAGTCGATTAAATTGCGCACAAGAGATGGCCCGGCGCGACAGTATTGGTGAAGt                             >  1:3111451/1‑71 (MQ=255)
                                       aGCTTGCGGCATTAAACAGTCGATTAAGTTGCGCACAAGAGAt                                                        >  1:1147155/1‑43 (MQ=255)
                                       aGCTTGCGGCATTAAACAGTCGATTAAATTGCGCACAAgaga                                                         >  1:1253186/1‑42 (MQ=255)
                                         cTTGCGGCATTAAACAGTCGATTAAATTGCGCACAAGAGATGGCCCGGCGCGACAGTATTGGTGAAGTtcc                          <  1:4483989/71‑1 (MQ=255)
                                            gCGGCATTAAACAGTCGATTAAATTGCGCACAAGAGATGGCCCGGCGCGACAGTATTGGTGAAGTtcctc                        <  1:3688330/70‑1 (MQ=255)
                                                  ttAAACAGTCGATTAAGTTGCGCACAAGAGATGGCCCGgcgc                                              <  1:1572602/42‑1 (MQ=255)
                                                   tAAACAGTCGATTAAATTGCGCACAAGAGATGGCCCGGCGCGACAGTAt                                      <  1:1003324/49‑1 (MQ=255)
                                                    aaaCAGTCGATTAAGTTGCGCACAAGAGATGGCCCGGCGCGACAGTATTGGTGAAg                              >  1:222241/1‑56 (MQ=255)
                                                    aaaCAGTCGATTAAATTGCGCACAAGAGATGGCCCGGCGCGACAGTATTGGTGAAGTtc                           >  1:2183490/1‑59 (MQ=255)
                                                    aaaCAGTCGATTAAATTGCGCACAAGAGATGGCCCGGCGCGACAGTATTGGTGAAGTTCCTCCTGTGCCGt               >  1:4010763/1‑71 (MQ=255)
                                                    aaaCAGTCGATTAAATTGCGCACAAGAGATGGCCCGGCGCGACAGTATTGGTGAAGTTCCTCCTGTGCCGt               >  1:1556638/1‑71 (MQ=255)
                                                     aaCAGTCGATTAAATTGCGCACAAGAGATGGCCCGGCGCGACAGTATTg                                    >  1:4374789/1‑49 (MQ=255)
                                                     aaCAGTCGATTAAATTGCGCACAAGAGATGGCCCGGCGCGACAGTATTGGTGAAGTTCCTCCTGTGCCGTg              >  1:857185/1‑71 (MQ=255)
                                                         gTCGATTAAGTTGCGCACAAGAGATGGCCCGGCGCGACAGTATTGGTGAAGTTCCTCCTGTGCCGTGgcgc          <  1:3705851/71‑1 (MQ=255)
                                                          tCGATTAAATTGCGCACAAGAGATGGCCCGGCGCGACAg                                         >  1:4603467/1‑39 (MQ=255)
                                                           cGATTAAATTGCGCACAAGAGATGGCCCGGCGCGACAGt                                        <  1:2840678/39‑1 (MQ=255)
                                                           cGATTAAATTGCGCACAAGAGATGGCCCGGCGCGACAGTa                                       >  1:3614241/1‑40 (MQ=255)
                                                            gATTAAGTTGCGCACAAGAGATGGCCCGGCGCGACAGTATTGGTGAAg                              >  1:2610266/1‑48 (MQ=255)
                                                            gATTAAGTTGCGCACAAGAGATGGCCCGGCGCGACAGTATTGGTGAAGTTCCTCCTGTGCCGTGGCGCa         <  1:870101/69‑1 (MQ=255)
                                                            gATTAAGTTGCGCACAAGAGATGGCCCGGCGCGACAGTATTGGTGAAGTTCCTCCTGTGACGTGGCGCACg       >  1:1643964/1‑71 (MQ=255)
                                                            gATTAAATTGCGCACAAGAGATGGCCCGGCGCGACAGTATTGGTGAAGTTCCTCCTGTGCCGTGGCGCACg       >  1:4242794/1‑71 (MQ=255)
                                                            gATTAAATTGCGCACAAGAGATGGCCCGGCGCGACAGTATTGGTGAAGTTCCTCCTGTGCCGTGGCGCACg       >  1:3710452/1‑71 (MQ=255)
                                                            gATTAAATTGCGCACAAGAGATGGCCCGGCGCGACAGTATTGGTGAAGTTCCTCCTGTGCCGTGGCGCACg       >  1:1101013/1‑71 (MQ=255)
                                                            gATTAAATTGCGCACAAGAGATGGCCCGGCGCGACAGTATTGGTGAAGTTCCTCCTGTGCCGTGGCGCACg       >  1:2980809/1‑71 (MQ=255)
                                                            gATTAAATTGCGCACAAGAGATGGCCCGGCGCGACAGTATTGGTGAAGTTCCTCCTGTGCCGTGGCGCACg       >  1:355125/1‑71 (MQ=255)
                                                             aTTAAGTTGCGCACAAGAGATGGCCCGGCGCGACAg                                         <  1:3516770/36‑1 (MQ=255)
                                                             aTTAAATTGCGCACAAGAGATGGCCCGGCGCGACAGTAtt                                     <  1:639340/40‑1 (MQ=255)
                                                               tAAATTGCGCACAAGAGATGGCCCGGCGCGACAGTATTGGTGAAGTTCCTCCTGTGCCGTGGCGCACGGTc    >  1:2613320/1‑71 (MQ=255)
                                                                 aaTTGCGCACAAGAGATGGCCCGGCGCGACAGTATTGGTGAAGTTCCTCCTGTGCCGTGGCGCACGGTCGt  <  1:3137589/71‑1 (MQ=255)
                                                                  |                                                                     
CCCGCGCCAGCCACTATAATGCCGGAGAATGCTTACATCAGCTTGCGGCATTAAACAGTCGATTAAATTGCGCACAAGAGATGGCCCGGCGCGACAGTATTGGTGAAGTTCCTCCTGTGCCGTGGCGCACGGTCGT  >  W3110S.gb/2213269‑2213404

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