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 2,002,183 G→A 23.2% R114C (CGC→TGC)  fliY ← cystine transporter subunit

Read alignment evidence...
  seq id position ref new freq score (cons/poly) reads annotation genes product
*W3110S.gb2,002,1830GA23.2% 136.4 / 38.4 69R114C (CGC→TGC) fliYcystine transporter subunit
Reads supporting (aligned to +/- strand):  ref base G (31/22);  new base A (4/12);  total (35/34)
Fisher's exact test for biased strand distribution p-value = 2.40e-02
Kolmogorov-Smirnov test that lower quality scores support variant p-value = 9.66e-01

TTACCTTTTTTCACCAGCGCCTGAATACCAGAAATGGTGTACGGGGTTGAGAAATCGTATTTTTTCTTGCGCTCATCAGAAATGGTGACCTGATTAATCACCACATCAATACGTTTAGAGTCCAGCGACGCCAGCATACCG  >  W3110S.gb/2002113‑2002253
                                                                      |                                                                      
ttACCTTTTTTCACCAGCGCCTGAATACCAGAAATGGTGTACGGGGTTGAGAAATCGTATTTTTTCTTgcg                                                                        <  1:3396252/71‑1 (MQ=255)
ttACCTTTTTTCACCAGCGCCTGAATACCAGAAATGGTGTACGGGGTTGAGAAATCGTATTTTTTCTTgcg                                                                        <  1:3467670/71‑1 (MQ=255)
     ttttttCACCAGCGCCTGAATACCAGAAATGGTGTACGGGGTTGAGAAATCGTATTTTTTCTTGCGCtcat                                                                   >  1:3626154/1‑71 (MQ=255)
       ttttCACCAGCGCCTGAATACCAGAAATGGTGTACGGGGTTGAGAAATCGTATTTTTTCTTGCGCtcat                                                                   >  1:2864428/1‑69 (MQ=255)
            aCCAGCGCCTGAATACCAGAAATGGTGTACGGGGTTGAGAAATCGTATTTTTTCTTGCACTCATCAGAAAt                                                            <  1:2432414/71‑1 (MQ=255)
              cAGCGCCTGAATACCAGAAATGGTGTACGGGGTTGAGAAATCGTATTTTTTCTTGCACTCATCAGAAATg                                                           <  1:4110347/70‑1 (MQ=255)
                gcgcCTGAATACCAGAAATGGTGTACGGGGTTGAGAAATCGTATTTTTTCTTGGACTCATCAGAAATGGTg                                                        <  1:4001539/71‑1 (MQ=255)
                      gAATACCAGAAATGGTGTACGGGGTTGAGAAATCGTATTTTTTCTTGCACtcatca                                                                 <  1:3512615/56‑1 (MQ=255)
                       aaTACCAGAAATGGTGTACGGGGTTGAGAAATCGTATTTTTTCTTGCGCTCATCAg                                                                >  1:2954882/1‑56 (MQ=255)
                       aaTACCAGAAATGGTGTACGGGGTTGAGAAATCGTATTTTTTCTTGCGCTCATCAg                                                                >  1:4448265/1‑56 (MQ=255)
                       aaTACCAGAAATGGTGTACGGGGTTGAGAAATCGTATTTTTTCTTGCGCTCATCAGAAATGGTGACCTg                                                   <  1:1174550/69‑1 (MQ=255)
                       aaTACCAGAAATGGTGTACGGGGTTGAGAAATCGTATTTTTTCTTGCGCTCATCAGAAATGGTGACCTGa                                                  <  1:2164311/70‑1 (MQ=255)
                       aaTACCAGAAATGGTGTACGGGGTTGAGAAATCGTATTTTTTCTTGCGCTCATCAGAAATGGTGACCTGAt                                                 >  1:2526816/1‑71 (MQ=255)
                       aaTACCAGAAATGGTGTACGGGGTTGAGAAATCGTATTTTTTCTTGCGCTCATCAGAAATGGTGACCTGAt                                                 >  1:3380281/1‑71 (MQ=255)
                         tACCAGAAATGGTGTACGGGGTTGAGAAATCGTATTTTTTCTTGCGCtc                                                                     <  1:370483/49‑1 (MQ=255)
                         tACCAGAAATGGTGTACGGGGTTGAGAAATCGTATTTTTTCTTGCGCTCATCAGa                                                               <  1:2755816/55‑1 (MQ=255)
                         tACCAGAAATGGTGTACGGGGTTGAGAAATCGTATTTTTTCCTGCACTCATCAGAAATGGTGACCTGATTa                                               <  1:4176039/71‑1 (MQ=255)
                           ccAGAAATGGTGTACGGGGTTGAGAAATCGTATTTTTTCTTGCGCTCATCAGAAATGGTGACCTGATTAAt                                             >  1:3199610/1‑71 (MQ=255)
                              gAAATGGTGTACGGGGTTGAGAAATCGTATTTTTTCTTGCGCTCATCAGAAATGGTGACCTGATTAATcac                                          <  1:2352277/71‑1 (MQ=255)
                                 aTGGTGTACGGGGTTGAGAAATCGTATTTTTTCTTgcgc                                                                       >  1:3001241/1‑39 (MQ=255)
                                 aTGGTGTACGGGGTTGAGAAATCGTATTTTTTCTTGCGCTCATCAGaa                                                              >  1:468476/1‑48 (MQ=255)
                                    gtgtACGGGGTTGAGAAATCGTATTTTTTCTTGCGCTCATCAGAAATGGTGACCTGATTAATCACCACAt                                     >  1:1007536/1‑70 (MQ=255)
                                     tgtACGGGGTTGAGAAATCGTATTTTTTCTTGCGCTCATCAGAAATgg                                                          <  1:1586860/48‑1 (MQ=255)
                                       tACGGGGTTGAGAAATCGTATTTTTTCTTGCACTCATCAGAAATGGTGACCTGATTaa                                              <  1:1151908/58‑1 (MQ=255)
                                         cGGGGTTGAGAAATCGTATTTTTTCTTGCGCTCATCAGaaa                                                             >  1:2355973/1‑41 (MQ=255)
                                         cGGGGTTGAGAAATCGTATTTTTTCTTGCGCTCATCAGaaa                                                             >  1:3490846/1‑41 (MQ=255)
                                         cGGGGTTGAGAAATCGTATTTTTTCTTGCGCTCATCAGAAATGGTGACCTGATTAATCACCACATCAATAc                               >  1:3584503/1‑71 (MQ=255)
                                         cGGGGTTGAGAAATCGTATTTTTTCTTGCGCTCATCAGAAATGGTGACCTGATTAATCACCACATCAATAc                               >  1:835062/1‑71 (MQ=255)
                                         cGGGGTTGAGAAATCGTATTTTTTCTTGCGCTCATCAGAAATGGTGACCTGATTAATCACCACATCAATAc                               >  1:4374142/1‑71 (MQ=255)
                                          ggggTTGAGAAATCGTATTTTTTCTTGCGCTCATCAGAAATGGTGACCTGATTAATCACCACATCAATACg                              >  1:564727/1‑71 (MQ=255)
                                          ggggTTGAGAAATCGTATTTTTTCTTGCACTCATCAGAAATGGTGACCTGATTAATc                                            <  1:2439650/57‑1 (MQ=255)
                                           gggTTGAGAAATCGTATTTTTTCTTGCGCTCATCAGAAATGGTGACCTGATTAATCACCACATCAATACGt                             >  1:4558513/1‑71 (MQ=255)
                                           gggTTGAGAAATCGTATTTTTTCTTGCGCTCATCAGAAATGGTGACCTGATTAATCACCACATCAATACGt                             >  1:1969363/1‑71 (MQ=255)
                                           gggTTGAGAAATCGTATTTTTTCTTGCGCTCATCAGAAATGGTGACCTGATTAATCACCACATCAATACGt                             >  1:602488/1‑71 (MQ=255)
                                            ggTTGAGAAATCGTATTTTTTCTTGCGCTCATCAg                                                                <  1:3689923/35‑1 (MQ=255)
                                            ggTTGAGAAATCGTATTTTTTCTTGCGCTCATCAGAAATGGTGACCTGATTAATCACCACATCAATACGtt                            <  1:2534199/71‑1 (MQ=255)
                                              ttGAGAAATCGTATTTTTTCTTGCGCTCATCAGAAAt                                                            <  1:3550145/37‑1 (MQ=255)
                                              ttGAGAAATCGTATTTTTTCTTGCGCTCATCAGAAATGGTGACCTGATTAATCACCACAt                                     <  1:2485184/60‑1 (MQ=255)
                                              ttGAGAAATCGTATTTTTTCTTGCGCTCATCAGAAATGGTGACCTGATTAATCACCACATCAATACGTTTa                          <  1:56531/71‑1 (MQ=255)
                                                gagaAATCGTATTTTTTCTTGCGCTCATCAGAAATg                                                           <  1:3375475/36‑1 (MQ=255)
                                                gagaAATCGTATTTTTTCTTGCACTCATCAGAAATGGTg                                                        <  1:455004/39‑1 (MQ=255)
                                                gagaAATCGTATTTTTTCTTGCACTCATCAGAAATGGTGa                                                       >  1:1008641/1‑40 (MQ=255)
                                                gagaAATCGTATTTTTTCTTGCACTCATCAGAAATGGTGCCCTGATTAATCACCACATCAATACGTTTa                          >  1:306307/1‑69 (MQ=255)
                                                 agaAATCGTATTTTTTCTTGCGCTCATCAGAAATGGTGACCTGa                                                  >  1:3234007/1‑44 (MQ=255)
                                                 agaAATCGTATTTTTTCTTGCGCTCATCAGAAATGGTGACCTGa                                                  >  1:111125/1‑44 (MQ=255)
                                                 agaAATCGTATTTTTTCTTGCGCTCATCAGAAATGGTGACCTGa                                                  >  1:4610477/1‑44 (MQ=255)
                                                  gaAATCGTATTTTTTCTTGCACTCATCAGAAATGGTGACCTGATTAATCACCACATCAATACGTTTAGAGt                      <  1:1947994/71‑1 (MQ=255)
                                                   aaaTCGTATTTTTTCTTGCGCTCATCAGAAATGGTGACCTGa                                                  >  1:2561947/1‑42 (MQ=255)
                                                   aaaTCGTATTTTTTCTTGCGCTCATCAGAAATGGTGACCTGa                                                  >  1:77275/1‑42 (MQ=255)
                                                   aaaTCGTATTTTTTCTTGCGCTCATCAGAAATGGTGACCTGa                                                  >  1:3624841/1‑42 (MQ=255)
                                                    aaTCGTATTTTTTCTTGCGCTCATCAGAAATGGTGACCTGATTAATcac                                          <  1:2980413/49‑1 (MQ=255)
                                                    aaTCGTATTTTTTCTTGCACTCATCAGAAATGGTGACCTGATTAATCACCACATCAATACGTTTAGAGTcc                    <  1:1149611/71‑1 (MQ=255)
                                                       cGTATTTTTTCTTGCACTCATCAGAAATGGTGACCTGATTAATCACCACATCAATACGTTTAGAGTCCAGc                 >  1:1053098/1‑71 (MQ=255)
                                                        gTATTTTTTCTTGCGCTCATCAGAAATGGTGACCTGATTAATCACCACATCAATACGTTTAGAGTCCAGCg                <  1:1689728/71‑1 (MQ=255)
                                                        gTATTTTTTCTTGCACTCATAAGAAATGGTGACCt                                                    >  1:3166288/1‑35 (MQ=38)
                                                          aTTTTTTCTTGCGCTCATCAGAAATGGTGACCTGATTAATca                                           >  1:1145790/1‑42 (MQ=255)
                                                          aTTTTTTCTTGCGCTCATCAGAAATGGTGACCTGATTAAGCACCACATCAATACGTTTAGAGTCCAGCGa               <  1:3461749/70‑1 (MQ=255)
                                                           ttttttCTTGCGCTCATCAGAAATGGTGACCTGATTAATCACCACATCAATACGTTTaga                        <  1:2264163/60‑1 (MQ=255)
                                                           ttttttCTTGCGCTCATCAGAAATGGTGACCTGATTAATCACCACATCAATACGTTTaga                        <  1:3464908/60‑1 (MQ=255)
                                                           ttttttCTTGCGCTCATCAGAAATGGTGACCTGATTAATCACCACATCAATACGTTTa                          <  1:2875347/58‑1 (MQ=255)
                                                           ttttttCTTGCGCTCATCAGAAATGGTGACCTGATTAATCACCACATCAATACGTTTa                          <  1:1511923/58‑1 (MQ=255)
                                                            tttttCTTGCGCTCATCAGAAATGGTGACCTGATTAATCACCACATCAATACGTTTa                          <  1:3178343/57‑1 (MQ=255)
                                                            tttttCTTGCGCTCATCAGAAATGGTGACCTGATTAATCACCACATCAATACGTTTAGAGTCCAGCGa               >  1:1876128/1‑68 (MQ=255)
                                                            tttttCTTGCACTCATCAGAAATGGTGACCTGATTa                                               <  1:4594413/36‑1 (MQ=255)
                                                            tttttCTTGCACTCATCAGAAATGGTGACCTGATTa                                               <  1:3663034/36‑1 (MQ=255)
                                                             ttttCTTGCGCTCATCAGAAATGGTGACCTGATTAAt                                             >  1:3183302/1‑37 (MQ=255)
                                                             ttttCTTGCGCTCATCAGAAATGGTGACCTGATTAATCACCACATCAATa                                >  1:2704306/1‑50 (MQ=255)
                                                             ttttCTTGCGCTCATCAGAAATGGTGACATGATTAAt                                             >  1:2746967/1‑37 (MQ=255)
                                                              tttCTTGCGCTCATCAGAAATGGTGACCTGATTAATCACCACATCAATACGt                             >  1:115372/1‑52 (MQ=255)
                                                                tCTTGCGCTCATCAGAAATGGTGACCTGATTAATCACCACATCaa                                  >  1:1359007/1‑45 (MQ=255)
                                                                tCTTGCGCTCATCAGAAATGGTGACCTGATTAATCACCACATCAATACGTTTAGAGTCCAGCGACGCCAg         <  1:2992521/70‑1 (MQ=255)
                                                                  ttGCGCTCATCAGAAATGGTGACCTGATTAATCACCACATCAATACGTTTa                          <  1:678528/51‑1 (MQ=255)
                                                                      gcTCATCAGAAATGGTGACCTGATTAATCACCACATCAATACGTTTAGAGTCCAGCGACGCCAGCATACCg  <  1:3055620/71‑1 (MQ=255)
                                                                      gcTCATCAGAAATGGTGACCTGATTAATCACCACATCAATACGTTTAGAGTCCAGCGACGCCAGCATACCg  <  1:1903177/71‑1 (MQ=255)
                                                                      gcTCATCAGAAATGGTGACCTGATTAATCACCACATCAATACGTTTAGAGTCCAGCGACGCCAGCATACCg  <  1:3060946/71‑1 (MQ=255)
                                                                      |                                                                      
TTACCTTTTTTCACCAGCGCCTGAATACCAGAAATGGTGTACGGGGTTGAGAAATCGTATTTTTTCTTGCGCTCATCAGAAATGGTGACCTGATTAATCACCACATCAATACGTTTAGAGTCCAGCGACGCCAGCATACCG  >  W3110S.gb/2002113‑2002253

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