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 F21 I0 R1 476 35.3 2812105 96.7% 2719305 61.2

Breseq alignment

BRESEQ :: Evidence
Predicted mutation
evidence seq id position mutation freq annotation gene description
RA W3110S.gb 2,983,818 A→G 9.8% V144A (GTG→GCG)  yqeF ← predicted acyltransferase

Read alignment evidence...
  seq id position ref new freq score (cons/poly) reads annotation genes product
*W3110S.gb2,983,8180AG 9.8% 182.8 / 11.7 71V144A (GTG→GCG) yqeFpredicted acyltransferase
Reads supporting (aligned to +/- strand):  ref base A (39/25);  new base G (4/3);  total (43/28)
Fisher's exact test for biased strand distribution p-value = 1.00e+00
Kolmogorov-Smirnov test that lower quality scores support variant p-value = 9.88e-01

TTCGCGAGCCAGATTTTCGGCGGTGACACCAATATGATAATCATTGAAGGCATCCCACAACCCATCATGCACAAGACTGTCAACCAACTGGCTATTGCCAAGCTGTGCACCGGTGCGGCTATCAGTCAGAACATGTG  >  W3110S.gb/2983748‑2983884
                                                                      |                                                                  
ttCGCGAGCCAGATTTTCGGCGGTGACACCAATATGATAATCATTGAAGGCATCCCACAACCCATCATGca                                                                    >  1:1398227/1‑71 (MQ=255)
      aGCCAGATTTTCGGCGGTGACACCAATATGATAATCATTGAAGGCATCCCACAACCCATCATGCACAAGa                                                               <  1:1480188/70‑1 (MQ=255)
       gCCAGATTTTCGGCGGTGACACCAATATGATAATCATTGAAGGCATCCCACAACCCATCATGCACaa                                                                 <  1:1440232/67‑1 (MQ=255)
        ccAGATTTTCGGCGGTGACACCAATATGATAATCATTGAAGGCATCCCACAACCCATCATGCACAAGACTg                                                            <  1:582259/71‑1 (MQ=255)
         cAGATTTTCGGCGGTGACACCAATATGATAATCATTGAAGGCATCCCACAACCCATCATGCACAAGACTGt                                                           >  1:2275404/1‑71 (MQ=255)
         cAGATTTTCGGCGGTGACACAAATATGATAATCATTGAAGGCATCCCACAACCCATCATGCACAAGACTGt                                                           >  1:1607417/1‑71 (MQ=255)
          aGATTTTCGGCGGTGACACCAATATGATAATCATTGAAGGCATCCCACAACCCATCATGCACAAGACTGTc                                                          <  1:1052748/71‑1 (MQ=255)
          aGATTTTCGGCGGTGACACCAATATGATAATCATTGAAGGCATCCCACAACCCATCATGCACAAGACTGTc                                                          <  1:2760610/71‑1 (MQ=255)
          aGATTTTCGGCGGTGACACCAATATGATAATCATTGAAGGCATCCCACAACCCATCATGCACAAGACTGTc                                                          <  1:1339487/71‑1 (MQ=255)
           gATTTTCGGCGGTGACACCAATATGATAATCATTGAAGGCATCCCACAACCCATCATGCACAAGACTGTc                                                          >  1:1914813/1‑70 (MQ=255)
            aTTTTCGGCGGTGACACCAATATGATAATCATTGAAGGCATCCCACAACCCATCATGCACAAGACTGTcaa                                                        >  1:642768/1‑71 (MQ=255)
             ttttCGGCGGTGACACCAATATGATAATCATTGAAGGCATCCCACAACCCATCATGCACAAGa                                                               >  1:275269/1‑63 (MQ=255)
               ttCGGCGGTGACACCAATATGATAATCATTGAAGGCATCCCACAACCCATCATGCACAAGACTGTcaacc                                                      >  1:712122/1‑70 (MQ=255)
                      gTGACACCAATATGATAATCATTGAAGGCATCCCACAACCCATCATGCACAAGACTGTCAACCAACTGGCt                                              <  1:1316335/71‑1 (MQ=255)
                      gTGACACCAATATGATAATCATTGAAGGCATCCCACAACCCATCATGCACAAGACTGTCAACCAACTGGCt                                              <  1:26124/71‑1 (MQ=255)
                        gACACCAATATGATAATCATTGAAGGCATCCCACAACCCATCATGCACAAGACTGTCAACCAACTGGCTa                                             <  1:970653/70‑1 (MQ=255)
                        gACACCAATATGATAATCATTGAAGGCATCCCACAACCCATCATGCACAAGACTGTCAACCAACTGGCTAt                                            >  1:496521/1‑71 (MQ=255)
                         acacCAATATGATAATCATTGAAGGCATCCCACAACCCATCATGCACAAGACTGTCAACCAACTGGCTAtt                                           >  1:2287537/1‑71 (MQ=255)
                         acacCAATATGATAATCATTGAAGGCATCCCACAACCCATCATGCACAAGACTGTCAACCAACTGGCTAtt                                           >  1:2281078/1‑71 (MQ=255)
                         acacCAATATGATAATCATTGAAGGCATCCCACAACCCATCATGCACAAGACTGTCAACCAACTGGCTAtt                                           >  1:2231347/1‑71 (MQ=255)
                              aaTATGATAATCATTGAAGGCATCCCACAACCCATCATGCACAAGACTg                                                            >  1:2579832/1‑49 (MQ=255)
                              aaTATGATAATCATTGAAGGCATCCCACAACCCATCATGCACAAGACTg                                                            >  1:372913/1‑49 (MQ=255)
                              aaTATGATAATCATTGAAGGCATCCCACAACCCATCATGCACAAGACTg                                                            >  1:443315/1‑49 (MQ=255)
                              aaTATGATAATCATTGAAGGCATCCCACAACCCATCATGCACAAGACTGTCAACCAACTGGCTATTGcc                                        >  1:169575/1‑69 (MQ=255)
                              aaTATGATAATCATTGAAGGCATCCCACAACCCATCATGCACAAGACTGTCAACCAACTGGCTATTGcc                                        >  1:1082912/1‑69 (MQ=255)
                              aaTATGATAATCATTGAAGGCATCCCACAAACCATCATGCACAAGa                                                               >  1:2628424/1‑46 (MQ=255)
                                tatGATAATCATTGAAGGCATCCCACAACCCATCATGCGCAAGACTg                                                            <  1:1931666/47‑1 (MQ=255)
                                 atGATAATCATTGAAGGCATCCCACAACCCATCATGCGCAAGACTGTCAACCAACTGGCTATTg                                          >  1:2010761/1‑64 (MQ=255)
                                 atGATAATCATTGAAGGCATCCCACAACCCATCATGCGCAAGACTGTCAACCAACTGGCTATTg                                          >  1:1265554/1‑64 (MQ=255)
                                 atGATAATCATTGAAGGCATCCCACAACCCATCATGCGCAAGACTGTCAACCAACTGGCTATTg                                          >  1:1414914/1‑64 (MQ=255)
                                  tgttAATCATTGAAGGCATCCCACAACCCATCATGCACAAGACTGTCAACCAACTGGCTATTGCCAAGCtg                                  >  1:2800770/4‑71 (MQ=255)
                                  tGATAATCATTGAAGGCATCCCACAACCCATCATGCACAAGACTGTCAACCAACTGGCTATTGCCAAGCtg                                  <  1:2598768/71‑1 (MQ=255)
                                   gATAATCATTGAAGGCATCCCACAACCCATCATGCACAAGACTGTCAACCAACTGGCTATTGCCAAGCtg                                  <  1:1255025/70‑1 (MQ=255)
                                    aTAATCATTGAAGGCATCCCACAACCCATCATGCACAAGACTGTcaaccaa                                                    >  1:186413/1‑51 (MQ=255)
                                      aaTCATTGAAGGCATCCCACAACCCATCATGCACAAGACTGTCAACCAACTGGCTAt                                            >  1:574083/1‑57 (MQ=255)
                                        tCATTGAAGGCATCCCACAACCCATCATGCACAAGACTGTcaacc                                                      <  1:472686/45‑1 (MQ=255)
                                        tCATTGAAGGCATCCCACAACCCATCATGCACAAGACTGTcaacc                                                      <  1:761389/45‑1 (MQ=255)
                                        tCATTGAAGGCATCCCACAACCCATCATGCACAAGACTGTcaacc                                                      <  1:764603/45‑1 (MQ=255)
                                        tCATTGAAGGCATCCCACAACCCATCATGCACAAGACTGTcaacc                                                      <  1:1775040/45‑1 (MQ=255)
                                        tCATTGAAGGCATCCCACAACCCATCATGCACAAGACTGTCAACCAACTGGc                                               <  1:704543/52‑1 (MQ=255)
                                        tCATTGAAGGCATCCCACAACCCATCATACACAAGACTGTCAACCAACTGGc                                               <  1:312464/52‑1 (MQ=255)
                                         cATTGAAGGCATCCCACAACCCATCATGCACAAGa                                                               >  1:129755/1‑35 (MQ=255)
                                         cATTGAAGGCATCCCACAACCCATCATGCACAAGa                                                               >  1:618378/1‑35 (MQ=255)
                                          aTTGAAGGCATCCCACAACCCATCATGCACAAGACTGTcaa                                                        >  1:1499552/1‑41 (MQ=255)
                                           ttGAAGGCATCCCACAACCCATCATGCACAAGACTGTcaacc                                                      <  1:1479516/42‑1 (MQ=255)
                                            tGAAGGCATCCCACAACCCATCATGCACAAGACTGTca                                                         >  1:377737/1‑38 (MQ=255)
                                            tGAAGGCATCCCACAACCCATCATGCACAAGACTGTca                                                         >  1:2207306/1‑38 (MQ=255)
                                             gAAGGCATCCCACAACCCATCATGCACAAGACTGTCAACCAACTGGCTATTGCCAAGCTGTGCACCGGTGc                       >  1:2377358/1‑71 (MQ=255)
                                                   aTCCCACAACCCATCATGCACAAGACTGTCAACCAACTGGCTATTGCCAAGCTGTGCACCGGTGCg                      <  1:2278808/66‑1 (MQ=255)
                                                   aTCCCACAACCCATCATGCACAAGACTGTCAACCAACTGGCTATTGCCAAGCTGTGCACCGGTGCGGCTAt                 <  1:722693/71‑1 (MQ=255)
                                                   aTCCCACAACCCATCATGCACAAGACTGTCAACCAACTGGCTATTGCCAAGCTGTGCACCGGTGCGGCTAt                 <  1:2808898/71‑1 (MQ=255)
                                                     cccACAACCCATCATGCACAAGACTGTCAACCAACTGGCTAt                                            >  1:1874067/1‑42 (MQ=255)
                                                      ccACAACCCATCATGCACAAGACTGTCAACCAACTGGCTa                                             >  1:904711/1‑40 (MQ=255)
                                                      ccACAACCCATCATGCACAAGACTGTCAACCAACTGGCTATTGCCAAGCTGTGCACCGGTGCGGCTAtcag              >  1:918228/1‑71 (MQ=255)
                                                      ccACAACCCATCATGCACAAGACTGTCAACCAACTGGCTATTGCCAAGCTGTGCACCGGTGCGGCTAtcag              >  1:517125/1‑71 (MQ=255)
                                                      ccACAACCCATCATGCACAAGACTGTCAACCAACTGGCTATTGCCAAGCTGTGCACCGGTGCGGCTAtcag              >  1:920993/1‑71 (MQ=255)
                                                      ccACAACCCATCATGCACAAGACTGTCAACCAACTGGCTATTGCCAAGCTGTGCACCGGTGCGGCTAtcag              >  1:895737/1‑71 (MQ=255)
                                                      ccACAACCCATCATGCACAAGACTGTCAACCAACTGGCTATTGCCAAGCTGTGCACCGGTGCGGCTAtcag              >  1:393529/1‑71 (MQ=255)
                                                      ccACAACCCATCATGCACAAGACTGTCAACCAACTGGCTATTGCCAAGCTGTGCACCGGTGCGGCTAtcag              >  1:743411/1‑71 (MQ=255)
                                                      ccACAACCCATCATGCACAAGACTGTCAACCAACTGGCTATTGCCAAGCTGTGCACCGGTGCGGCTAtca               >  1:515452/1‑70 (MQ=255)
                                                       cacaACCCATCATGCACAAGACTGTCAACCAACTGGc                                               <  1:1979623/37‑1 (MQ=255)
                                                         caACCCATCATGCGCAAGACTGTCAACCAACTGGCTATTGCCAAGCTGTGCACCGGTGCGGCTAtcagtca           <  1:2269182/71‑1 (MQ=255)
                                                         caACCCATCATGCACAAGACTGTCAACCAACTGGCTATTGCCAAGCTGTGCACCGGTGCGGCTAtcagt             >  1:2749412/1‑69 (MQ=255)
                                                           aCCCATCATGCACAAGACTGTCAACCAACTGGCTATTGCCAAGCTGTGCACCGGTGCGGCTAtcagtcag          >  1:2627641/1‑70 (MQ=255)
                                                                tcatGCGCAAGACTGTCAACCAACTGGCTATTGCCAAGCtg                                  <  1:801004/41‑1 (MQ=255)
                                                                  atGCGCAAGACTGTCAACCAACTGGCTATTGCCAAGCTGTGCACCGGTGCGGCTATCAGTCAGAACAtgtg  >  1:1046482/1‑71 (MQ=255)
                                                                  atGCACAAGACTGTCAACCAACTGGCTATTGCCAAGCtgtg                                >  1:2173691/1‑41 (MQ=255)
                                                                  atGCACAAGACTGTCAACCAACTGGCTATTGCCAAGCTGTGCAc                             >  1:1307600/1‑44 (MQ=255)
                                                                  atGCACAAGACTGTCAACCAACTGGCTATTGCCAAGCTGTGCACCGGTGCGGCTATCAGTCAGAACAtgtg  >  1:1902365/1‑71 (MQ=255)
                                                                  atGCACAAGACTGTCAACCAACTGGCTATTGCCAAGCTGTGCACCGGTGCGGCTATCAGTCAGAACAtgt   <  1:1789317/70‑1 (MQ=255)
                                                                  atGCACAAGACTGTCAACCAACTGGCTATTGCCAAGCTGTGCACCGGTGCGGCTATCAGTCAGAACAtgt   <  1:639990/70‑1 (MQ=255)
                                                                   tGCACAAGACTGTCAACCAACTGGCTATTGCCAAGCTGTGCACCGGTGCGGCTATCAGTCAGAACAtgtg  <  1:2155058/70‑1 (MQ=255)
                                                                     cacaAGACTGTCAACCAACTGGCTATTGCCAAGCTGTGCAcc                            <  1:733097/42‑1 (MQ=255)
                                                                     cacaAGACTGTCAACCAACTGGCTATTGCCAAGCTGTGCAcc                            <  1:1667978/42‑1 (MQ=255)
                                                                     cacaAGACTGTCAACCAACTGGCTATTGCCAAGCTGTGCACCGGTGCGGCTATCAGTCAGaa        >  1:2259985/1‑62 (MQ=255)
                                                                      |                                                                  
TTCGCGAGCCAGATTTTCGGCGGTGACACCAATATGATAATCATTGAAGGCATCCCACAACCCATCATGCACAAGACTGTCAACCAACTGGCTATTGCCAAGCTGTGCACCGGTGCGGCTATCAGTCAGAACATGTG  >  W3110S.gb/2983748‑2983884

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