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 4,527,342 C→T 8.9% E479K (GAG→AAG)  yjhG ← predicted dehydratase

Read alignment evidence...
  seq id position ref new freq score (cons/poly) reads annotation genes product
*W3110S.gb4,527,3420CT 8.9% 202.5 / 8.2 67E479K (GAG→AAG) yjhGpredicted dehydratase
Reads supporting (aligned to +/- strand):  ref base C (29/32);  new base T (4/2);  total (33/34)
Fisher's exact test for biased strand distribution p-value = 4.27e-01
Kolmogorov-Smirnov test that lower quality scores support variant p-value = 8.66e-01

ACGCCAATAATGACCAGAATATCGCCCGCCTTGATCTTGTCATGTTTGATATCGTAAATCGCACTTTTCTCGGACAGATAAACCTTCGCCACACCTTTATGGTAATAGATACCTTGCTCATCAATCATCGAGGGGTC  >  W3110S.gb/4527272‑4527408
                                                                      |                                                                  
aCGCCAATAATGACCAGAATATCGCCCGCCTTGATCTTGTCATGTTTGATATCGTAAATCGCACTTTtctc                                                                    >  1:85696/1‑71 (MQ=255)
aCGCCAATAATGACCAGAATATCGCCCGCCTTGATCTTGTCATGTTTGATATCGTAAATCGCACTTTtctc                                                                    >  1:331291/1‑71 (MQ=255)
 cGCCAATAATGACCAGAATATCGCCCGCCTTGATCTTGTCATGTTTGATATCGTAAATCGCACTTTTCTCg                                                                   <  1:3528083/71‑1 (MQ=255)
  gCCAATAATGACCAGAATATCGCCCGCCTTGATCTTGTCATGTTTGATATCGTAAATCGCACTTTTCTCgg                                                                  <  1:949127/71‑1 (MQ=255)
  gCCAATAATGACCAGAATATCGCCCGCCTTGATCTTGTCATGTTTGATATCGTAAATCGCACTTTTCTCg                                                                   >  1:3884042/1‑70 (MQ=255)
  gCCAATAATGACCAGAATATCGCCCGCCTTGATCTTGTCATGTTTGATATCGTAAATCGCACTTTTCTCg                                                                   >  1:2185729/1‑70 (MQ=255)
      ataatGACCAGAATATCGCCCGCCTTGATCTTGTCATGTTTGATATCGTAAATCGCACTTTTCTCGGa                                                                 >  1:353600/1‑68 (MQ=255)
       taatGACCAGAATATCGCCCGCCTTGATCTTGTCATGTTTGATATCGTAAATCGCACTTTTCTCGGa                                                                 >  1:202271/1‑67 (MQ=255)
       taatGACCAGAATATCGCCCGCCTTGATCTTGTCATGTTTGATATCGTAAATCGCACTTTTCTCGGACAGa                                                             <  1:1517346/71‑1 (MQ=255)
       taatGACCAGAATATCGCCCGCCTTGATCTTGTCATGTTTGATATCGTAAATCGCACTTTTCTCGGACAGa                                                             <  1:1682390/71‑1 (MQ=255)
        aatGACCAGAATATCGCCCGCCTTGATCTTGTCATGTTTGATATCGTAAATCGCACTTTTCTCGGACAg                                                              >  1:3786575/1‑69 (MQ=255)
        aatGACCAGAATATCGCCCGCCTTGATCTTGTCATGTTTGATATCGTAAATCGCACTTTTCTCGGACAGa                                                             >  1:2769776/1‑70 (MQ=255)
          tGACCAGAATATCGCCCGCCTTGATCTTGTCATGTTTGATATCGTAAATCGCACTTTTCTCGGACAGATaa                                                          <  1:1279546/71‑1 (MQ=255)
          tGACCAGAATATCGCCCGCCTTGATCTTGTCATGTTTGATATCGTAAATCGCACTTTTCTCGGACAGATaa                                                          <  1:2987820/71‑1 (MQ=255)
                  atatCGCCCGCCTTGATCTTGTCATGTTTGATATCGTAAATCGCACTTTTCTCGGACAGATAAACCTTCGc                                                  <  1:2871582/71‑1 (MQ=255)
                   tatCGCCCGCCTTGATCTTGTCATGTTTGATATCGTAAATCGCACTTTTCTCGGACAGATAAAc                                                        >  1:1038095/1‑64 (MQ=255)
                   tatCGCCCGCCTTGATCTTGTCATGTTTGATATCGTAAATCGCACTTTTCTCGGACAGATAAACCTTCGc                                                  >  1:3423392/1‑70 (MQ=255)
                     tCGCCCGCCTTGATCTTGTCATGTTTGATATCGTAAATCGCACTTTTCTCGGa                                                                 >  1:2883578/1‑53 (MQ=255)
                     tCGCCCGCCTTGATCTTGTCATGTTTGATATCGTAAATCGCACTTTTCTCGGACAGATAAACCTTCGCcac                                               <  1:4427658/71‑1 (MQ=255)
                     tCGCCCGCCTTGATCTTGTCATGTTTGATATCGTAAATCGCACTTTTCTCGGACAGATAAACCTTCGCcac                                               <  1:3036734/71‑1 (MQ=255)
                      cgcccgccTTGATCTTGTCATGTTTGATATCGTAAATCGCACTTTTCTCGGACAGATa                                                           <  1:901121/58‑1 (MQ=255)
                       gcccgccTTGATCTTGTCATGTTTGATATCGTAAATCGCACTTTTCTCGGACAGATAAACCTTCGCCacac                                             <  1:2313088/71‑1 (MQ=255)
                        cccgccTTGATCTTGTCATGTTTGATTTCGTAAATCGCACTTTTCTCGGACAGATAAACCTTc                                                    <  1:3354505/63‑1 (MQ=255)
                          cgccTTGATCTTGTCATGTTTGATATCGTAAATCGCACTTTTCTCGGACAGATAAACCTTCGCCACACCtt                                          >  1:2041367/1‑71 (MQ=255)
                          cgccTTGATCTTGTCATGTTTGATATCGTAAATCGCACTTTTCTCGGACAGATAAACCTTCGCCACACCtt                                          <  1:2069508/71‑1 (MQ=255)
                          cgccTTGATCTTGTCATGTTTGATATCGTAAATCGCACTTTTCTCGGACAGATAAACCTTCGCCACACCtt                                          >  1:2314670/1‑71 (MQ=255)
                          cgccTTGATCTTGTCATGTTTGATATCGTAAATCGCACTTTTCTCGGACAGATAAACCTTCGCCACACCt                                           >  1:1836752/1‑70 (MQ=255)
                            ccTTGATCTTGTCATGTTTGATATCGTAAATCGCACTTTTCTCGGACAGATAAACCTTCGCCACACCTTTa                                        <  1:2864309/71‑1 (MQ=255)
                             cTTGATCTTGTCATGTTTGATATCGTAAATCGCACTTTTCTCGGACAGATa                                                           >  1:2529438/1‑51 (MQ=255)
                                gATCTTGTCATGTTTGATATCGTAAATCGCACTTTTCTCGGACAGATAAACCTTCGCca                                                >  1:3951321/1‑59 (MQ=255)
                                gATCTTGTCATGTTTGATATCGTAAATCGCACTTTTCTCGGACAGATAAACCTTCGCCACACCTTTATgg                                     >  1:1640575/1‑70 (MQ=255)
                                gATCTTGACATGTTTGATATCGTAAATCGCACTTTTCTCGGACAGATAAACCTTCGCca                                                >  1:381041/1‑59 (MQ=255)
                                 aTCTTGTCATGTTTGATATCGTAAATCGCACTTTTCTTgg                                                                  >  1:4118876/1‑40 (MQ=255)
                                 aTCTTGTCATGTTTGATATCGTAAATCGCACTTTTCTTgg                                                                  >  1:3030308/1‑40 (MQ=255)
                                 aTCTTGTCATGTTTGATATCGTAAATCGCACTTTTCTCGGACAGATAAACCTTCGCCACACCTTTATgg                                     >  1:3820281/1‑69 (MQ=255)
                                    ttGTCATGTTTGATATCGTAAATCGCACTTTTCTTGGACAGATAAACCTTCGCCACACCTTTATGGTaa                                  >  1:4368612/1‑69 (MQ=255)
                                    ttGTCATGTTTGATATCGTAAATCGCACTTTTCTCGGACAGATAAACCtt                                                     >  1:3728053/1‑50 (MQ=255)
                                    ttGTCATGTTTGATATCGTAAATCGCACTTTTCTCGGACAGATAAACCTTCGCca                                                >  1:1012240/1‑55 (MQ=255)
                                      gTCATGTTTGATATCGTAAATCGCACTTTTCTCGGACAGATAAAcc                                                       >  1:1705218/1‑46 (MQ=255)
                                      gTCATGTTTGATATCGTAAATCGCACTTTTCTCGGACAGATAAACCTTCGCCACACCTTTATGGTAATa                                <  1:3869775/69‑1 (MQ=255)
                                       tCATGTTTGATATCGTAAATCGCACTTTTCTCGGACAGATAAACCTTCGCCACACCTTTATGGTAATa                                <  1:3537496/68‑1 (MQ=255)
                                       tCATGTTTGATATCGTAAATCGCACTTTTCTCGGACAGATAAACCTTCGCCACACCTTTATGGTAATAGa                              <  1:1888145/70‑1 (MQ=255)
                                       tCATGTTTGATATCGTAAATCGCACTTTTCTCGGACAGATAAACCTTCGCCACACCTTTATGGTAATAGa                              <  1:4260612/70‑1 (MQ=255)
                                       tCATGTTTGATATCGTAAATCGCACTTTTCTCGGACAGATAAACCTTCGCCACACCTTTATGGTAATAGAt                             <  1:2519033/71‑1 (MQ=255)
                                         aTGTTTGATATCGTAAATCGCACTTTTCTCGGACAGATAAACCt                                                      >  1:498209/1‑44 (MQ=255)
                                         aTGTTTGATATCGTAAATCGCACTTTTCTCGGACAGATAAACCt                                                      >  1:492787/1‑44 (MQ=255)
                                          tGTTTGATATCGTAAATCGCACTTTTCTTGGACAGATAAACCTTCGCCACACCTTTATGGTaa                                  <  1:2549530/63‑1 (MQ=255)
                                            tttGATATCGTAAATCGCACTTTTCTCGGACAGATaaa                                                         >  1:2125712/1‑38 (MQ=255)
                                                 tatCGTAAATCGCACTTTTCTCGGACAGATAAACCTTCGCCACACCTTTATGGTAATAGa                              <  1:1105901/60‑1 (MQ=255)
                                                     gTAAATCGCACTTTTCTTGGACAGATAAACCTTCGCCACACCTTTATGGTAAt                                 >  1:1217494/1‑53 (MQ=255)
                                                     gTAAATCGCACTTTTCTCGGACAGATAAACCTTCGCCACACCttt                                         <  1:1973812/45‑1 (MQ=255)
                                                     gTAAATCGCACTTTTCTCGGACAGATAAACCTTCGCCACACCttt                                         <  1:2846563/45‑1 (MQ=255)
                                                      tAAATCGCACTTTTCTCGGACAGATAAACCTTCGCCACACCTTTATGGTAATAGAt                             <  1:1847748/56‑1 (MQ=255)
                                                        aaTCGCACTTTTCTCGGACAGATAAACCTTCGCCACACCTTTATgg                                     >  1:214686/1‑46 (MQ=255)
                                                        aaTCGCACTTTTCTCGGACAGATAAACCTTCGCCACACCTTTATgg                                     >  1:3256645/1‑46 (MQ=255)
                                                        aaTCGCACTTTTCTCGGACAGATAAACCTTCGCCACACCTTTATGGTAATAGa                              >  1:380582/1‑53 (MQ=255)
                                                         aTCGCACTTTTCTCGGACAGATAAACCTTCGCCACACCTTTATGGTAATAGAt                             <  1:3799729/53‑1 (MQ=255)
                                                          tCGCACTTTTCTCGGACAGATAAACCTTCGCCACACCttt                                         <  1:1521815/40‑1 (MQ=255)
                                                          tCGCACTTTTCTCGGACAGATAAACCTTCGCCACACCTTTATGGt                                    <  1:877829/45‑1 (MQ=255)
                                                          tCGCACTTTTCTCGGACAGATAAACCTTCGCCACACCTTTATGGTAATAGATACCTTGCTCATCAatcatc          <  1:3030220/71‑1 (MQ=255)
                                                          tCGCACTTTTCTCGGACAGATAAACCTTCGCCACACCTTTATGGTAATAGATACCTTGCTCATCAatcatc          <  1:62255/71‑1 (MQ=255)
                                                            gCACTTTTCTCGGACAGATAAACCTTCGCCACACCTTTATGGTAATAGATACCTTGCTCATCAatcat           >  1:2541639/1‑68 (MQ=255)
                                                            gCACTTTTCTCGGACAGATAAACCTTCGCCACACCTTTATGGTAATAGATACCTTGCTCATCAATCATCg         <  1:4205865/70‑1 (MQ=255)
                                                               cTTTTCTTGGACAGATAAACCTTCGCCACACCTTTATGGTAATAGATACCTTGCTCATCAATCATCGAggg     <  1:1939556/71‑1 (MQ=255)
                                                                ttttCTCGGACAGATAAACCTTCGCCACACCTTTATg                                      <  1:4557022/37‑1 (MQ=255)
                                                                ttttCTCGGACAGATAAACCTTCGCCACACCTTTATGGTAATAGATACCTTGCtca                   <  1:3949119/56‑1 (MQ=255)
                                                                ttttCTCGGACAGATAAACCTTCGCCACACCTTTATGGTAATAGATACCTTGCTCATCAatcatc          <  1:1361207/65‑1 (MQ=255)
                                                                  ttCTCGGACAGATAAACCTTCGCCACACCTTTATGGTAATAGATACCTTGCTCATCAATCATCGAGGGGt   >  1:3495158/1‑70 (MQ=255)
                                                                  ttCTCGGACAGATAAACCTTCGCCACACCTTTATGGTAATAGATACCTTGCTCATCAATCATCGAGGGGt   >  1:2538973/1‑70 (MQ=255)
                                                                   tctcGGACAGATAAACCTTCGCCACACCTTTATGGTAATAGATACCTTGCTCATCAATCATCGAGGGGTc  <  1:3209426/70‑1 (MQ=255)
                                                                    ctcGGACAGATAAACCTTCGCCACACCTTTATGGTAATAGa                              >  1:4118122/1‑41 (MQ=255)
                                                                    ctcGGACAGATAAACCTTAGCCACACCTTTATGGTAATAGa                              >  1:554980/1‑41 (MQ=255)
                                                                      |                                                                  
ACGCCAATAATGACCAGAATATCGCCCGCCTTGATCTTGTCATGTTTGATATCGTAAATCGCACTTTTCTCGGACAGATAAACCTTCGCCACACCTTTATGGTAATAGATACCTTGCTCATCAATCATCGAGGGGTC  >  W3110S.gb/4527272‑4527408

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