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 F21 I0 R2 316 65.6 5147759 97.4% 5013917 60.3

Breseq alignment

BRESEQ :: Evidence
Predicted mutation
evidence seq id position mutation freq annotation gene description
RA W3110S.gb 459,715 A→G 20.5% Y535C (TAC→TGC)  lon → DNA‑binding ATP‑dependent protease La

Read alignment evidence...
  seq id position ref new freq score (cons/poly) reads annotation genes product
*W3110S.gb459,7150AG20.5% 156.1 / 35.4 73Y535C (TAC→TGC) lonDNA‑binding ATP‑dependent protease La
Reads supporting (aligned to +/- strand):  ref base A (22/36);  new base G (11/4);  total (33/40)
Fisher's exact test for biased strand distribution p-value = 1.98e-02
Kolmogorov-Smirnov test that lower quality scores support variant p-value = 1.00e+00

GTAATGCACTGAAAAAAGGTGAGCTGACCGTCGACGATAGCGCCATTATCGGCATTATTCGTTACTACACCCGTGAGGCGGGCGTGCGTGGTCTGGAGCGTGAAATCTCCAAACTGTGTCGCAAAGCGGTTAAGC  >  W3110S.gb/459649‑459783
                                                                  |                                                                    
gTAATGCACTGAAAAAAGGTGAGCTGACCGTCGACGATAGCGCCATTATCGGCATTATTCGTTACTACAcc                                                                  <  1:299734/71‑1 (MQ=255)
   aTGCACTGAAAAAAGGTGAGCTGACCGTCGACGATAGCGCCATTATCGGCATTATTCGTTACTACACCCGt                                                               <  1:2716624/71‑1 (MQ=255)
   aTGCACTGAAAAAAGGTGAGCTGACCGTCGACGATAGCGCCATTATCGGCATTATTCGTTACTACACCCGt                                                               <  1:1864216/71‑1 (MQ=255)
    tGCACTGAAATAAGGTGAGCTGACCGTCGACGATAGCGCCATTATCGGCATTATTCGTTACTACACCCGt                                                               <  1:5113762/70‑1 (MQ=255)
     gCACTGAAAAAAGGTGAGCTGACCGTCGACGATAGCGCCATTATCGGCATTATTCGTTACTACACCCGt                                                               >  1:1016618/1‑69 (MQ=255)
      cACTGAAAAAAGGTGAGCTGACCGTCGACGATAGCGCCATTATCGGCATTATTCGTTACTACACCCGTGAg                                                            <  1:3293260/71‑1 (MQ=255)
      cACTGAAAAAAGGTGAGCTGACCGTCGACGATAGCGCCATTATCGGCATTATTCGTTACTACACCCGTGAg                                                            >  1:1603808/1‑71 (MQ=255)
          gAAAAAAGGTGAGCTGACCGTCGACGATAGCGCCATTATCGGCATTATTCGTTACTACACCCGTGAggcgg                                                        >  1:1576592/1‑71 (MQ=255)
          gAAAAAAGGTGAGCTGACCGTCGACGATAGCGCCATTATCGGCATTATTCGTTACTACACCCGTGAggcgg                                                        >  1:160986/1‑71 (MQ=255)
               aaGGTGAGCTGACCGTCGACGATAGCGCCATTATCGGCATTATTCGTTACTGCACCCGTGAGGCGGgcgtg                                                   >  1:4071010/1‑71 (MQ=255)
               aaGGTGAGCTGACCGTCGACGATAGCGCCATTATCGGCATTATTCGTTACTGCACCCGTGAGGCGGgcgtg                                                   >  1:5093061/1‑71 (MQ=255)
               aaGGTGAGCTGACCGTCGACGATAGCGCCATTATCGGCATTATTCGTTACTGCACCCGTGAGGCGGgcgt                                                    >  1:4470806/1‑70 (MQ=255)
               aaGGTGAGCTGACCGTCGACGATAGCGCCATTATCGGCATTATTCGTTACTACACCCGTGAGGCGGgcgtg                                                   <  1:500304/71‑1 (MQ=255)
                 ggTGAGCTGACCGTCGACGATAGCGCCATTATCGGCATTATTCGTTACTACACCCGTGAGGCGGgcgtgcg                                                 >  1:4172102/1‑71 (MQ=255)
                  gTGAGCTGACCGTCGACGATAGCGCCATTATCGGCATTATTCGTTACTGCACCCGt                                                               <  1:2702622/56‑1 (MQ=255)
                    gAGCTGACCGTCGACGATAGCGCCATTATCGGCATTATTCGTTACTACACCCGTGAGGCGGGCGTGCGTgg                                              >  1:4844241/1‑71 (MQ=255)
                      gCTGACCGTCGACGATAGCGCCATTATCGGCATTATTCGTTACTACACCCGTGAGGCGGGCGTGCGTGGTc                                            >  1:4741813/1‑71 (MQ=255)
                        tGACCGTCGACGATAGCGCCATTATCGGCATTATTCGTTACTGCACCCGTGa                                                             >  1:2960865/1‑52 (MQ=255)
                         gACCGTCGACGATAGCGCCATTATCGGCATTATTCGTTACTGCACCCg                                                                >  1:4622040/1‑48 (MQ=255)
                         gACCGTCGACGATAGCGCCATTATCGGCATTATTCGTTACTGCACCCGTGAGGCGGGcgtgcgtg                                               >  1:444616/1‑65 (MQ=255)
                         gACCGTCGACGATAGCGCCATTATCGGCATTATTCGTTACTACACCCGTGAgg                                                           <  1:4812490/53‑1 (MQ=255)
                         gACCGTCGACGATAGCGCCATTATCGGCATTATTCGTTACTACACCCGTGAGGCGGGCGTGCGTGGTCTg                                          >  1:3121779/1‑70 (MQ=255)
                         gACCGTCGACGATAGCACCATTATCGGCATTATTCGTTACTACACCCGTGAgg                                                           <  1:4750450/53‑1 (MQ=255)
                          aCCGTCGACGATAGCGCCATTATCGGCATTATTCGTTACTACACCCGTGAGGCGGGCGTGCGTGGTCTg                                          <  1:3367964/69‑1 (MQ=255)
                          aCCGTCGACGATAGCGCCATTATCGGCATTATTCGTTACTACACCCGTGAGGCGGGCGTGCGTGGTCTg                                          <  1:334748/69‑1 (MQ=255)
                          aCCGTCGACGATAGCGCCATTATCGGCATTATTCGTTACTACACCCGTGAGGCGGGCGTGCGTGGTCTg                                          <  1:3169056/69‑1 (MQ=255)
                              tCGACGATAGCGCCATTATCGGCATTATTCGTTACTACACCCGt                                                               <  1:563268/44‑1 (MQ=255)
                              tCGACGATAGCGCCATTATCGGCATTATTCGTTACTACACCCGt                                                               <  1:915536/44‑1 (MQ=255)
                                gacgaTAGCGCCATTATCGGCATTATTCGTTACTACACCCGTGa                                                             >  1:1794506/1‑44 (MQ=255)
                                gacgaTAGCGCAATTATCGGCATTATTCGTTACTACACCCGTGAGGCGGGCGTGCGTGGTCTGGAGCGTGa                                  <  1:722837/71‑1 (MQ=255)
                                 acgaTAGCGCCATTATCGGCATTATTCGTTACTACACCCGTGAGGCGGGCGTGCGTGGTCTGGAGCGTGaa                                 <  1:4048525/71‑1 (MQ=255)
                                  cgaTAGCGCCATTATCGGCATTATTCGTTACTACACCCGTGAGGCGGGCGTGCGTGGTCTGGAGCGTGaaa                                <  1:4700493/71‑1 (MQ=255)
                                   gaTAGCGCCATTATCGGCATTATTCGTTACTGCACCCGTGAGGCGGGCGTGCGTGGTCTGGAGCGTGAAAt                               >  1:519217/1‑71 (MQ=255)
                                   gaTAGCGCCATTATCGGCATTATTCGTTACTGCACCCGTGAGGCGGGCGTGCGTGGTCTGGAGCGTGAAAt                               >  1:3470469/1‑71 (MQ=255)
                                    aTAGCGCCATTATCGGCATTATTCGTTACTACACCCGTGa                                                             <  1:3036997/40‑1 (MQ=255)
                                    aTAGCGCCATTATCGGCATTATTCGTTACTACACCCGTGa                                                             <  1:2541915/40‑1 (MQ=255)
                                    aTAGCGCCATTATCGGCATTATTCGTTACTACACCCGTGa                                                             <  1:376931/40‑1 (MQ=255)
                                    aTAGCGCCATTATCGGCATTATTCGTTACTACACCCGTGAGGCGGGCGTGCGTgg                                              <  1:136333/55‑1 (MQ=255)
                                      aGCGCCATTATCGGCATTATTCGTTACTACACCCGTGAGGCGGGCGTGCGTGGTc                                            >  1:3021625/1‑55 (MQ=255)
                                      aGCGCCATTATCGGCATTATTCGTTACTACACCCGTGAGGCGGGCGTGCGTGGTCTGGAGCGTGAAAtctc                            >  1:978217/1‑71 (MQ=255)
                                       gcgcCATTATCGGCATTATTCGTTACTACACCCGTGAGGCGGGCGTGCGTGGTCTg                                          <  1:3515686/56‑1 (MQ=255)
                                       gcgcCATTATCGGCATTATTCGTTACTACACCCGTGAGGCGGGCGTGCGTGGTCTGGAGCGTg                                   <  1:3918432/63‑1 (MQ=255)
                                       gcgcCATTATCGGCATTATTCGTTACTACACCCGTGAGGCGGGCGTGCGTGGTCTGGAGCGTg                                   <  1:553538/63‑1 (MQ=255)
                                         gcCATTATCGGCATTATTCGTTACTGCACCCGTGAGGCGGGCGTGCGTGGTCTGGAGCGTGAAATCTCCaa                         <  1:2698184/71‑1 (MQ=255)
                                            aTTATCGGCATTATTCGTTACTACACCCGTGAGGCGGGCGTGCGTGGTCTGGAGCGTGAAATCTCCAAACt                      >  1:3255246/1‑71 (MQ=255)
                                            aTTATCGGCATTATTCGTTACTACACCCGTGAGGCGGGCGTGCGTGGTCTGGAGCGTGAAATCTCCAAACt                      <  1:1151184/71‑1 (MQ=255)
                                            aTTATCGGCATTATTCGTTACTACACCCGTGAGGCGGGCGTGCGTGGTCTGGAGCGTGAAATCTCCAAACt                      <  1:1369052/71‑1 (MQ=255)
                                            aTTATCGGCATTATTCGTTACTACACCCGTGAGGCGGGCGTGCGTGGTCTGGAGCGTGAAATCTCCAAACt                      >  1:5074286/1‑71 (MQ=255)
                                             ttATCGGCATTATTCGTTACTGCACCCGTGAGGCGGGCGTGCGTGGTCTGGAGCGTGAAATCTCCa                          <  1:544198/66‑1 (MQ=255)
                                             ttATCGGCATTATTCGTTACTACACCCGTGAGGCGGGCGTGCGTgg                                              <  1:987838/46‑1 (MQ=255)
                                             ttATCGGCATTATTCGTTACTACACCCGTGAGGAGGGCGTGCGTgg                                              <  1:1485436/46‑1 (MQ=255)
                                              tATCGGCATTATTCGTTACTACACCCGTGAGGCGGGCGTGCGTGGTCTGGAGCGTGAAATCTCCAAACtgt                    >  1:3621971/1‑71 (MQ=255)
                                               aTCGGCATTATTCGTTACTACACCCGTGAGGCGGgcgtgcgt                                                >  1:3500171/1‑42 (MQ=255)
                                               aTCGGCATTATTCGTTACTACACCCGTGAGGCGGGCGTGCGTGGTc                                            >  1:4559074/1‑46 (MQ=255)
                                               aTCGGCATTATTCGTTACTACACCCGTGAGGCGGGCGTGCGTGGTc                                            >  1:1394115/1‑46 (MQ=255)
                                                tCGGCATTATTCGTTACTGCACCCGTGAGGCGGGCGTGCGTGGTCTGGAGCGTGAAATCTCCAAACTgtgt                  <  1:2977291/71‑1 (MQ=255)
                                                tCGGCATTATTCGTTACTACACCCGTGAggcgggc                                                      <  1:2778918/35‑1 (MQ=255)
                                                 cGGCATTATTCGTTACTACACCCGTGAGGCGGGCGTGCGTGGTCTGGAGCGTGAAATCTCCaaa                        >  1:1089587/1‑64 (MQ=255)
                                                   gCATTATTCGTTACTACACCCGTGAGGCGGGCGTGCGTGGTCTGGAGCGTGAAATCTCCAAACTGTGTCGc               <  1:4943717/71‑1 (MQ=255)
                                                     attattCGTTACTGCACCCGTGAGGCGGgcgtgcgt                                                >  1:676334/1‑36 (MQ=255)
                                                     attattCGTTACTGCACCCGTGAGGCGGGCGTGCGTGGTCTGGAGCGTGAAATCTCCAAACTGTGTCGCa              >  1:854109/1‑70 (MQ=255)
                                                      ttattCGTTACTACACCCGTGAGGCGGGCGTGCGTGGTCTGGAGCGTGAAATCTCCAAACTGTGTCGc               <  1:3339407/68‑1 (MQ=255)
                                                      ttattCGTTACTACACCCGTGAGGCGGGCGTGCGTGGTCTGGAGCGTGAAATCTCCAAACTGTGTCGc               <  1:1943436/68‑1 (MQ=255)
                                                      ttattCGTTACTACACCCGTGAGGCGGGCGTGCGTGGTCTGGAGCGTGAAATCTCCAAACTGTGTCGCaaa            <  1:567883/71‑1 (MQ=255)
                                                      ttattCGTTACTACACCCGTGAGGCGGGCGTGCGTGGTCTGGAGCGTGAAATCTCCAAACTGTGTCGCaaa            <  1:4118705/71‑1 (MQ=255)
                                                      ttattCGTTACTACACCCGTGAGGCGGGCGTGCGTGGTCTGGAGCGTGAAATCTCCAAACTGTGTCGCaaa            <  1:1511377/71‑1 (MQ=255)
                                                       tattCGTTACTACACCCGTGAGGCGGGCGTGCGTGGTCTGGAGCGTGaa                                 <  1:2431395/49‑1 (MQ=255)
                                                       tattCGTTACTACACCCGTGAGGCGGGCGTGCGTGGTCTGGAGCGTGaa                                 <  1:1266539/49‑1 (MQ=255)
                                                        attCGTTACTACACCCGTGAGGCGGGCGTGCGTGGTCTGGAGCGTGAAAt                               >  1:1601287/1‑50 (MQ=255)
                                                        attCGTTACTACACCCGTGAGGCGGGCGTGCGTGGTCTGGAGCGTGAAAt                               >  1:67338/1‑50 (MQ=255)
                                                        attCGTTACTACACCCGTGAGGCGGGCGTGCGTGGTCTGGAGCGTGAAATCTCCAAACTGTGTCGCaaa            >  1:2574532/1‑69 (MQ=255)
                                                        attCGTTACTACACCCGTGAGGCGGGCGTGCGTGGTCTGGAGCGTGAAATCTCCAAACTGTGTCGCaa             >  1:2625450/1‑68 (MQ=255)
                                                         ttCGTTACTGCACCCGTGAGGCGGGCGTGCGTGGTGTGGAGCGTGAAATCTCCAAACTGTGTCGCAAAGCg         >  1:2485695/1‑71 (MQ=255)
                                                              tactacACCCGTGAGGCGGGCGTGCGTGGTCTGGAGCGTGAAATCTCCAAACTGTGTCGCAAAGCGGtt      >  1:3494861/1‑69 (MQ=255)
                                                               actgcACCCGTGAGGCGGGCGTGCGTGGTCTGGAGCGTGAAATCTCCAAACTGTGTCGCAAAGCGGTTAAg   >  1:2706301/1‑71 (MQ=255)
                                                                ctacACCCGTGAGGCGGGCGTGCGTGGTCTGGAGCGTGAAATCTCCAAACTGTGTCGCAAAGCGGTTAAGc  <  1:907523/71‑1 (MQ=255)
                                                                  |                                                                    
GTAATGCACTGAAAAAAGGTGAGCTGACCGTCGACGATAGCGCCATTATCGGCATTATTCGTTACTACACCCGTGAGGCGGGCGTGCGTGGTCTGGAGCGTGAAATCTCCAAACTGTGTCGCAAAGCGGTTAAGC  >  W3110S.gb/459649‑459783

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