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
A11 F142 I1 R1 99 64.8 3148104 96.3% 3031624 99.9

Breseq alignment

BRESEQ :: Evidence
Predicted mutation
evidence seq id position mutation annotation gene description
RA NC_000913 3,910,662 A→T D288E (GAT→GAA)  pstS ← phosphate ABC transporter periplasmic binding protein

Read alignment evidence...
  seq id position ref new freq score (cons/poly) reads annotation genes product
*NC_0009133,910,6620AT100.0% 215.6 / NA 61D288E (GAT→GAA) pstSphosphate ABC transporter periplasmic binding protein
Reads supporting (aligned to +/- strand):  ref base A (0/0);  new base T (30/31);  total (30/31)

CTGGCGTAATCCAGGTCGTTCGCCTGTTTAGCCCCGGTTTTGTACGCCCAGTCGAAGAATTTCAGCACTTCTGTGCCTTGTTCTGGTTTCTTCTGATCTTTGTGGATCAGAATGAACGTGGTAGAGGTAATAGGCCATGCATCTTCGCCTTTCTGGTTGGTCAGATCCTGAGCGAAGGTTTTGCTCCAGTC  >  NC_000913/3910567‑3910757
                                                                                               |                                                                                               
cTGGCGTAATCCAGGTCGTTCGCCTGTTTAGCCCCGGTTTTGTACGCCCAGTCGAAGAATTTCAGCACTTCTGTGCCTTGTTCTGGTTTCTTCTGTTCtt                                                                                             <  2:1450817/100‑1 (MQ=255)
   gCGTAATCCAGGTCGTTCGCCTGTTTAGCCCCGGTTTTGTACGCCCAGTCGAAGAATTTCAGCACTTCTGTGCCTTGTTCTGGTTTCTTCTGTTCTTtgt                                                                                          <  2:144101/100‑1 (MQ=255)
     gTAATCCAGGTCGTTCGCCTGTTTAGCCCCGGTTTTGTACGCCCAGTCGAAGAATTTCAGCACTTCTGTGCCTTGTTCTGGTTTCTTCTGTTCTTTGTgg                                                                                        <  2:742654/100‑1 (MQ=255)
     gTAATCCAGGTCGTTCGCCTGTTTAGCCCCGGTTTTGTACGCCCAGTCGAAGAATTTCAGCACTTCTGTGCCTTGTTCTGGTTTCTTCTGTTCTTTGTgg                                                                                        <  2:1093532/100‑1 (MQ=255)
     gTAATCCAGGTCGTTCGCCTGTTTAGCCCCGGTTTTGTACGCCCAGTCGAAGAATTTCAGCACTTCTGTGCCTTGTTCTGGTTTCTTCTGTTCTTTGTgg                                                                                        <  2:1543778/100‑1 (MQ=255)
      tAATCCAGGTCGTTCGCCTGTTTAGCCCCGGTTTTGTACGCCCAGTCGAAGAATTTCAGCACTTCTGTGCCTTGTTCTGGTTTCTTCTGTTCTTTGTGGa                                                                                       >  2:616610/1‑100 (MQ=255)
        aTCCAGGTCGTTCGCCTGTTTAGCCCCGGTTTTGTACGCCCAGTCGAAGAATTTCAGCACTTCTGTGCCTTGTTCTGGTTTCTTCTGTTCTTTGTGGATc                                                                                     <  2:510536/100‑1 (MQ=255)
        aTCCAGGTCGTTCGCCTGTTTAGCCCCGGTTTTGTACGCCCAGTCGAAGAATTTCAGCACTTCTGTGCCTTGTTCTGGTTTCTTCTGTTCTTTGTGGATc                                                                                     >  2:432590/1‑100 (MQ=255)
        aTCCAGGTCGTTCGCCTGTTTAGCCCCGGTTTTGTACGCCCAGTCGAAGAATTTCAGCACTTCTGTGCCTTGTTCTGGTTTCTTCTGTTCTTTGTGGATc                                                                                     <  2:815391/100‑1 (MQ=255)
         tCCAGGTCGTTCGCCTGTTTAGCCCCGGTTTTGTACGCCCAGTCGAAGAATTTCAGCACTTCTGTGCCTTGTTCTGGTTTCTTCTGTTCTTTGTGGATCa                                                                                    <  2:817189/100‑1 (MQ=255)
         tCCAGGTCGTTCGCCTGTTTAGCCCCGGTTTTGTACGCCCAGTCGAAGAATTTCAGCACTTCTGTGCCTTGTTCTGGTTTCTTCTGTTCTTTGTGGATCa                                                                                    <  2:1026553/100‑1 (MQ=255)
         tCCAGGTCGTTCGCCTGTTTAGCCCCGGTTTTGTACGCCCAGTCGAAGAATTTCAGCACTTCTGTGCCTTGTTCTGGTTTCTTCTGTTCTTTGTGGATCa                                                                                    <  2:69490/100‑1 (MQ=255)
             ggTCGTTCGCCTGTTTAGCCCCGGTTTTGTACGCCCAGTCGAAGAATTTCAGCACTTCTGTGCCTTGTTCTGGTTTCTTCTGTTCTTTGTGGATCAGAAt                                                                                <  2:308245/100‑1 (MQ=255)
                   tCGCCTGTTTAGCCCCGGTTTTGTACGCCCAGTCGAAGAATTTCAGCACTTCTGTGCCTTGTTCTGGTTTCTTCTGTTCTTTGTGGATCAGAATGAACGt                                                                          >  1:330084/1‑100 (MQ=255)
                    cGCCTGTTTAGCCCCGGTTTTGTACGCCCAGTCGAAGAATTTCAGCACTTCTGTGCCTTGTTCTGGTTTCTTCTGTTCTTTGTGGATCAGAATGAACGTg                                                                         >  1:671926/1‑100 (MQ=255)
                         gTTTAGCCCCGGTTTTGTACGCCCAGTCGAAGAATTTCAGCACTTCTGTGCCTTGTTCTGGTTTCTTCTGTTCTTTGTGGATCAGAATGAACGTGGTaga                                                                    <  2:1118083/100‑1 (MQ=255)
                         cgatctccccGGTTTTGTACGCCCAGTCGAAGAATTTCAGCACTTCTGTGCCTTGTTCTGGTTTCTTCTGTTCTTTGTGGATCAGAATGAACGTGGTaga                                                                    <  2:1532932/94‑1 (MQ=255)
                           ttAGCCCCGGTTTTGTACGCCCAGTCGAAGAATTTCAGCACTTCTGTGCCTTGTTCTGGTTTCTTCTGTTCTTTGTGGATCAGAATGAACGTGGTAGAgg                                                                  <  1:1566731/100‑1 (MQ=255)
                            tAGCCCCGGTTTTGTACGCCCAGTCGAAGAATTTCAGCACTTCTGTGCCTTGTTCTGGTTTCTTCTGTTCTTTGTGGATCAGAATGAACGTGGTAGAGGt                                                                 >  2:1507527/1‑100 (MQ=255)
                               ccccGGTTTTGTACGCCCAGTCGAAGAATTTCAGCACTTCTGTGCCTTGTTCTGGTTTCTTCTGTTCTTTGTGGATCAGAATGAACGTGGTagaagatcg                                                              >  1:1532942/1‑94 (MQ=255)
                                cccGGTTTTGTACGCCCAGTCGAAGAATTTCAGCACTTCTGTGCCTTGTTCTGGTTTCTTCTGTTCTTTGTGGATCAGAATGAACGTGGTAGAGGTAATa                                                             >  2:348244/1‑100 (MQ=255)
                                  cGGTTTTGTACGCCCAGTCGAAGAATTTCAGCACTTCTGTGCCTTGTTCTGGTTTCTTCTGTTCTTTGTGGATCAGAATGAACGTGGTAGAGGTAATAgg                                                           >  1:727890/1‑100 (MQ=255)
                                   ggTTTTGTACGCCCAGTCGAAGAATTTCAGCACTTCTGTGCCTTGTTCTGGTTTCTTCTGTTCTTTGTGGATCAGAATGAACGTGGTAGAGGTAATAGGc                                                          <  1:1389546/100‑1 (MQ=255)
                                    gTTTTGTACGCCCAGTCGAAGAATTTCAGCACTTCTGTGCCTTGTTCTGGTTTCTTCTGTTCTTTGTGGATCAGAATGAACGTGGTAGAGGTAATAGGcc                                                         <  1:263547/100‑1 (MQ=255)
                                    gTTTTGTACGCCCAGTCGAAGAATTTCAGCACTTCTGTGCCTTGTTCTGGTTTCTTCTGTTCTTTGTGGATCAGAATGAACGTGGTAGAGGTAATAGGcc                                                         >  1:219026/1‑100 (MQ=255)
                                     ttttGTACGCCCAGTCGAAGAATTTCAGCACTTCTGTGCCTTGTTCTGGTTTCTTCTGTTCTTTGTGGATCAGAATGAACGTGGTAGAGGTAATAGGCCa                                                        <  2:672083/100‑1 (MQ=255)
                                         gTACGCCCAGTCGAAGAATTTCAGCACTTCTGTGCCTTGTTCTGGTTTCTTCTGTTCTTTGTGGATCAGAATGAACGTGGTAGAGGTAATAGGCCATGct                                                    <  1:1230256/100‑2 (MQ=255)
                                         gTACGCCCAGTCGAAGAATTTCAGCACTTCTGTGCCTTGTTCTGGTTTCTTCTGTTCTTTGTGGATCAGAATGAACGTGGTAGAGGTAATAGGCCATGct                                                    <  2:593154/100‑2 (MQ=255)
                                           aCGCCCAGTCGAAGAATTTCAGCACTTCTGTGCCTTGTTCTGGTTTCTTCTGTTCTTTGTGGATCAGAATGAACGTGGTAGAGGTAATAGGCCATGCTTc                                                  <  1:1360908/100‑1 (MQ=255)
                                            ngCCCAGTCGAAGAATTTCAGCACTTCTGTGCCTTGTTCTGGTTTCTTCTGTTCTTTGTGGATCAGAATGAACGTGGTAGAGGTAATAGGCCATGCTTCt                                                 >  2:479499/2‑100 (MQ=255)
                                            cGCCCAGTCGAAGAATTTCAGCACTTCTGTGCCTTGTTCTGGTTTCTTCTGTTCTTTGTGGATCAGAATGAACGTGGTAGAGGTAATAGGCCATGCTTCt                                                 >  2:554742/1‑100 (MQ=255)
                                            cGCCCAGTCGAAGAATTTCAGCACTTCTGTGCCTTGTTCTGGTTTCTTCTGTTCTTTGTGGATCAGAATGAACGTGGTAGAGGTAATAGGCCATGCTTCt                                                 >  2:1171418/1‑100 (MQ=255)
                                            cGCCCAGTCGAAGAATTTCAGCACTTCTGTGCCTTGTTCTGGTTTCTTCTGTTCTTTGTGGATCAGAATGAACGTGGCAGAGGTAATAGGCCATGCTTc                                                  >  2:111745/1‑99 (MQ=255)
                                              cccAGTCGAAGAATTTCAGCACTTCTGTGCCTTGTTCTGGTTTCTTCTGTTCTTTGTGGATCAGAATGAACGTGGTAGAGGTAATAGGCCATGCttcttc                                               >  2:980857/1‑100 (MQ=255)
                                              cccAGTCGAAGAATTTCAGCACTTCTGTGCCTTGTTCTGGTTTCTTCTGTTCTTTGTGGATCAGAATGAACGTGGTAGAGGTAATAGGCCATGCttcttc                                               <  1:915549/100‑1 (MQ=255)
                                               ccAGTCGAAGAATTTCAGCACTTCTGTGCCTTGTTCTGGTTTCTTCTGTTCTTTGTGGATCAGAATGAACGTGGTAGAGGTAATAGGCCATGCTTCTTCg                                              <  1:1533847/100‑1 (MQ=255)
                                                     gaagaaTTTCAGCACTTCTGTGCCTTGTTCTGGTTTCTTCTGTTCTTTGTGGATCAGAATGAACGTGGTAGAGGTAATAGGCCATGCTTCTTCGCCTTTc                                        >  2:393813/1‑100 (MQ=255)
                                                          aTTTCAGCACTTCTGTGCCTTGTTCTGGTTTCTTCTGTTCTTTGTGGATCAGAATGAACGTGGTAGAGGTAATAGGCCATGCTTCTTCGCCTTTCtggtt                                   >  2:1511566/1‑100 (MQ=255)
                                                          aTTTCAGCACTTCTGTGCCTTGTTCTGGTTTCTTCTGTTCTTTGTGGATCAGAATGAACGTGGTAGAGGTAATAGGCCATGCTTCTTCGCCTTTCtggtt                                   >  1:1317469/1‑100 (MQ=255)
                                                           tttCAGCACTTCTGTGCCTTGTTCTGGTTTCTTCTGTTCTTTGTGGATCAGAATGAACGTGGTAGAGGTAATAGGCCATGCTTCTTCGCCTTTCtggttg                                  <  1:980865/100‑1 (MQ=255)
                                                            ttCAGCACTTCTGTGCCTTGTTCTGGTTTCTTCTGTTCTTTGTGGATCAGAATGAACGTGGTAGAGGTAATAGGCCATGCTTCTTCGCCTTTCtggttgg                                 <  1:723249/100‑1 (MQ=255)
                                                             tCAGCACTTCTGTGCCTTGTTCTGGTTTCTTCTGTTCTTTGTGGATCAGAATGAACGTGGTAGAGGTAATAGGCCATGCTTCTTCGCCTTTCtggttggt                                <  1:115491/100‑1 (MQ=255)
                                                              cAGCACTTCTGTGCCTTGTTCTGGTTTCTTCTGTTCTTTGTGGATCAGAATGAACGTGGTAGAGGTAATAGGCCATGCTTCTTCGCCTTTCTGGTTGGTc                               >  2:1539524/1‑100 (MQ=255)
                                                               aGCACTTCTGTGCCTTGTTCTGGTTTCTTCTGTTCTTTGTGGATCAGAATGAACGTGGTAGAGGTAATAGGCCATGCTTCTTCGCCTTTCTGGTTGGTCa                              <  1:709058/100‑1 (MQ=255)
                                                               aGCACTTCTGTGCCTTGTTCTGGTTTCTTCTGTTCTTTGTGGATCAGAATGAACGTGGTAGAGGTAATAGGCCATGCTTCTTCGCCTTTCTGGTTGGTCa                              >  1:293127/1‑100 (MQ=255)
                                                                    ttCTGTGCCTTGTTCTGGTTTCTTCTGTTCTTTGTGGATCAGAATGAACGTGGTAGAGGTAATAGGCCATGCTTCTTCGCCTTTCTGGTTGGTCAGATcc                         <  1:616613/100‑1 (MQ=255)
                                                                     tCTGTGCCTTGTTCTGGTTTCTTCTGTTCTTTGTGGATCAGAATGAACGTGGTAGAGGTAATAGGCCATGCTTCTTCGCCTTTCTGGTTGGTCAGATCCt                        >  1:1175917/1‑100 (MQ=255)
                                                                        gtgCCTTGTTCTGGTTTCTTCTGTTCTTTGTGGATCAGAATGAACGTGGTAGAGGTAATACGCCATGCTTCTTCGCCTTTCTGGTTGGTCAGATCCTGAg                     >  2:795574/1‑100 (MQ=255)
                                                                         tgCCTTGTTCTGGTTTCTTCTGTTCTTTGTGGATCAGAATGAACGTGGTAGAGGTAATAGGCCATGCTTCTTCGCCTTTCTGGTTGGTCAGATCCTGAGc                    <  2:1317460/100‑1 (MQ=255)
                                                                            cTTGTTCTGGTTTCTTCTGTTCTTTGTGGATCAGAATGAACGTGGTAGAGGTAATAGGCCATGCTTCTTCGCCTTTCTGGTTGGTCAGATCCTGAGCGaa                 >  2:55075/1‑100 (MQ=255)
                                                                            cTTGTTCTGGTTTCTTCTGTTCTTTGTGGATCAGAATGAACGTGGTAGAGGTAATAGGCCATGCTTCTACGCCTTTCAGGTTGGTCAGATCCTGAGCGaa                 >  2:1061775/1‑100 (MQ=255)
                                                                             ttGTTCTGGTTTCTTCTGTTCTTTGTGGATCAGAATGAACGTGGTAGAGGTAATAGGCCATGCTTCTTCGCCTTTCTGGTTGGTCAGATCCTGAGCGAAg                <  2:715109/100‑1 (MQ=255)
                                                                             ttGTTCTGGTTTCTTCTGTTCTTTGTGGATCAGAATGAACGTGGTAGAGGTAATAGGCCATGCTTCTTCGCCTTTCTGGTTGGTCAGATCCTGAGCGAAg                <  1:1192404/100‑1 (MQ=255)
                                                                                  cTGGTTTCTTCTGTTCTTTGTGGATCAGAATGAACGTGGTAGAGGTAATAGGCCATGCTTCTTCGCCTTTCTGGTTGGTCAGATCCTGAGCGAAGGtttt           >  2:69145/1‑100 (MQ=255)
                                                                                    ggTTTCTTCTGTTCTTTGTGGATCAGAATGAACGTGGTAGAGGTAATAGGCCATGCTTCTTCGCCTTTCTGGTTTGTCAGATCCTGAGCGAAGGTTTTGc         >  2:869121/1‑100 (MQ=255)
                                                                                    ggTTTCTTCTGTTCTTTGTGGATCAGAATGAACGTGGTAGAGGTAATAGGCCATACTTCTTCGCCTTTCTGGTTGGTCAGATCCTGAGCGAAGGTTTTGc         >  2:839574/1‑100 (MQ=255)
                                                                                     gTTTCTTCTGTTCTTTGTGGATCAGAATGAACGTGGTAGAGGTAATAGGCCATGCTTCTTCGCCTTTCTGGTTGGTCAGATCCTGAGCGAAGGTTTTGCt        >  2:158329/1‑100 (MQ=255)
                                                                                       ttcttcTGTTCTTTGTGGATCAGAATGAACGTGGTAGAGGTAATAGGCCATGCTTCTTCGCCTTTCTGGTTGGTCAGATCCTGAGCGAAGGTTTTGCTcn      <  1:607715/100‑2 (MQ=255)
                                                                                         cttctGTTCTTTGTGGATCAGAATGAACGTGGTAGAGGTAATAGGCCATGCTTCTTCGCCTTTCTGGTTGGTCAGATCCTGAGCGAAGGTTTTGCTCCAg    >  1:1201375/1‑100 (MQ=255)
                                                                                          ttctGTTCTTTGTGGATCAGAATGAACGTGGTAGAGGTAATAGGCCATGCTTCTTCGCCTTTCTGGTTGGTCAGATCCTGAGCGAAGGTTTTGCTCCAGt   >  1:141420/1‑100 (MQ=255)
                                                                                           tctGTTCTTTGTGGATCAGAATGAACGTGGTAGAGGTAATAGGCCATGCTTCTTCGCCTTTCTGGTTGGTCAGATCCTGAGCGAAGGTTTTGCTCCAGTc  >  1:1508310/1‑100 (MQ=255)
                                                                                               |                                                                                               
CTGGCGTAATCCAGGTCGTTCGCCTGTTTAGCCCCGGTTTTGTACGCCCAGTCGAAGAATTTCAGCACTTCTGTGCCTTGTTCTGGTTTCTTCTGATCTTTGTGGATCAGAATGAACGTGGTAGAGGTAATAGGCCATGCATCTTCGCCTTTCTGGTTGGTCAGATCCTGAGCGAAGGTTTTGCTCCAGTC  >  NC_000913/3910567‑3910757

Alignment Legend
Aligned base mismatch/match (shaded by quality score): ATCG/ATCG < 3 ≤ ATCG/ATCG < 27 ≤ ATCG/ATCG < 37 ≤ ATCG/ATCG < 41 ≤ ATCG/ATCG
Unaligned base: atcg    Masked matching base: atcg    Alignment gap: ‑    Deleted base: ‑

GATK/CNVnator alignment

N/A