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
A91 F1 I1 R1 18 55.4 3661525 95.1% 3482110 76.0

Breseq alignment

BRESEQ :: Evidence
Predicted mutation
evidence seq id position mutation annotation gene description
RA REL606 3,911,972 (T)7→6 intergenic (‑173/‑150) yifB ← / → ilvL predicted bifunctional enzyme and transcriptional regulator/ilvG operon leader peptide

Read alignment evidence...
  seq id position ref new freq score (cons/poly) reads annotation genes product
*REL6063,911,9660T.89.7% 305.1 / 32.7 78intergenic (‑167/‑156)yifB/ilvLpredicted bifunctional enzyme and transcriptional regulator/ilvG operon leader peptide
Reads supporting (aligned to +/- strand):  ref base T (3/5);  new base . (29/41);  total (32/46)
Fisher's exact test for biased strand distribution p-value = 1.00e+00
Kolmogorov-Smirnov test that lower quality scores support variant p-value = 9.98e-01

TGATGCTCGCAAAAATGCAGCGGACAAAGGATGAACTACGAGGAAGGGAACAACATTCATACTGAAATTGAATTTTTTTCACTCACTATTTTATTTTTAAAAAACAACAATTTATATTGAAATTATTAAACGCATCATAAA  >  REL606/3911894‑3912034
                                                                        |                                                                    
tgatgCTCGCAAAAATGCAGCGGACAAAGGATGAACTACGAGGAAGGGAACAACATTCATACTGAAATTGAAtttt                                                                   <  1:40836/76‑1 (MQ=255)
    gCTCGCAAAAATGCAGCGGACAAAGGATGAACTACGAGGAAGGGAACAACATTCATACTGAAATTGAAttttttca                                                               <  2:530116/76‑3 (MQ=255)
    gCTCGCAAAAATGCAGCGGACAAAGGATGAACTACGAGGAAGGGAACAACATTCATACTGAAATTGAAttttttca                                                               <  1:163954/76‑3 (MQ=255)
       cGCAAAAATGCAGCGGACAAAGGATGAACTACGAGGAAGGGAACAACATTCATACTGAAATTGAA‑TTTTTtcactc                                                           >  1:1562975/1‑76 (MQ=255)
        gCAAAAATGCAGCGGACAAAGGATGAACTACGAGGAAGGGAACAACATTCATACTGAAATTGAA‑TTTTTtcactca                                                          <  1:1793468/76‑1 (MQ=255)
           aaaaTGCAGCGGACAAAGGATGAACTACGAGGAAGGGAACAACATTCATACTGAAATTGAA‑TTTTTTCACTCACta                                                       >  2:1024084/1‑76 (MQ=255)
            aaaTGCAGCGGACAAAGGATGAACTACGAGGAAGGGAACAACATTCATACTGAAATTGAA‑TTTTTTCACTCACtat                                                      >  1:1609692/1‑76 (MQ=255)
            aaaTGCAGCGGACAAAGGATGAACTACGAGGAAGGGAACAACATTCATACTGAAATTGAA‑TTTTTTCACTCACtat                                                      >  1:916763/1‑76 (MQ=255)
             aaTGCAGCGGACAAAGGATGAACTACGAGGAAGGGAACAACATTCATACTGAAATTGAA‑TTTTTTCACTCACtatt                                                     <  1:875963/76‑1 (MQ=255)
              aTGCAGCGGACAAAGGATGAACTACGAGGAAGGGAACAACATTCATACTGAAATTGAA‑TTTTTTCACTCACtattt                                                    <  2:670090/76‑1 (MQ=255)
              aTGCAGCGGACAAAGGATGAACTACGAGGAAGGGAACAACATTCATACTGAAATTGAA‑TTTGTTCACTCACtattt                                                    <  1:986528/76‑1 (MQ=255)
               tGCAGCGGACAAAGGATGAACTACGAGGAAGGGAACAACATTCATACTGAAATTGAA‑TTTTTTCACTCACtatttt                                                   <  1:1626250/76‑1 (MQ=255)
                 cAGCGGACAAAGGATGAACTACGAGGAAGGGAACAACATTCATACTGAAATTGAA‑TTTTTTCACTCACtattttat                                                 >  1:206509/1‑76 (MQ=255)
                 cAGCGGACAAAGGATGAACTACGAGGAAGGGAACAACATTCATACTGAAATTGAA‑TTTTTTCACTCACtattttat                                                 >  1:136332/1‑76 (MQ=255)
                  aGCGGACAAAGGATGAACTACGAGGAAGGGAACAACATTCATACTGAAATTGAA‑TTTTTTCACTCACtattttatt                                                <  1:1168294/76‑1 (MQ=255)
                   gCGGACAAAGGATGAACTACGAGGAAGGGAACAACATTCATACTGAAATTGAA‑TTTTTTCACTCACtattttattt                                               <  2:374403/76‑1 (MQ=255)
                    cGGACAAAGGATGAACTACGAGGAAGGGAACAACATTCATACTGAAATTGAATTTTTTTCACTCACtattttattt                                               >  2:177316/1‑76 (MQ=255)
                       aCAAAGGATGAACTACGAGGAAGGGAACAACATTCATACTGAAATTGAA‑TTTTTTCACTCACTATTTTATTTTTaa                                           <  1:32585/76‑1 (MQ=255)
                        cAAAGGATGAACTACGAGGAAGGGAACAACATTCATACTGAAATTGAA‑TTTTTTCACTCACTATTTTATTTTTaaa                                          <  2:485749/76‑1 (MQ=255)
                        cAAAGGATGAACTACGAGGAAGGGAACAACATTCATACTGAAATTGAA‑TTTTTTCACTCACTATTTTATTTTTaaa                                          <  1:1061373/76‑1 (MQ=255)
                         aaaGGATGAACTACGAGGAAGGGAACAACATTCATACTGAAATTGAA‑TTTTTTCACTCACTATTTTATTTTTaaaa                                         <  2:177431/76‑1 (MQ=255)
                         aaaGGATGAACTACGAGGAAGGGAACAACATTCATACTGAAATTGAA‑TTTTTTCACTCACTATTTTATTTTTaaaa                                         <  1:791558/76‑1 (MQ=255)
                          aaGGATGAACTACGAGGAAGGGAACAACATTCATACTGAAATTGAA‑TTTTTTCACTCACTATTTTATTTTTaaaaa                                        <  2:141981/76‑1 (MQ=255)
                           aGGATGAACTACGAGGAAGGGAACAACATTCATACTGAAATTGAA‑TTTTTTCACTCACTATTTTATTTTTaaaaaa                                       <  1:388774/76‑1 (MQ=255)
                           aGGATGAACTACGAGGAAGGGAACAACATTCATACTGAAATTGAA‑TTTTTTCACTCACTATTTTATTTTTaaaaaa                                       >  1:290986/1‑76 (MQ=255)
                            ggATGAACTACGAGGAAGGGAACAACATTCATACTGAAATTGAA‑TTTTTTCACTCACTATTTTATTTTTAAAAaac                                      <  2:1565802/76‑1 (MQ=255)
                            ggATGAACTACGAGGAAGGGAACAACATTCATACTGAAATTGAA‑TTTTTTCACTCACTATTTTATTTTTAAAAaac                                      <  1:356747/76‑1 (MQ=255)
                             gATGAACTACGAGGAAGGGAACAACATTCATACTGAAATTGAATTTTTTTCACTCACTATTTTATTTTTAAAAaac                                      <  1:1202383/76‑1 (MQ=255)
                              aTGAACTACGAGGAAGGGAACAACATTCATACTGAAATTGAA‑TTTTTTCACTCACTATTTTATTTTTAAAAaacaa                                    >  2:995335/1‑76 (MQ=255)
                               tGAACTACGAGGAAGGGAACAACATTCATACTGAAATTGAA‑TTTTTTCACTCACTATTTTATTTTTAAAAaacaac                                   <  2:568907/76‑1 (MQ=255)
                                gAACTACGAGGAAGGGAACAACATTCATACTGAAATTGAA‑TTTTTTCACTCACTATTTTATTTTTAAAAAacaaca                                  <  1:1536974/76‑1 (MQ=255)
                                 aaCTACGAGGAAGGGAACAACATTCATACTGAAATTGAA‑TTTTTTCACTCACTATTTTATTTTTAAAAAAcaacaa                                 >  2:399893/1‑76 (MQ=255)
                                 aaCTACGAGGAAGGGAACAACATTCATACTGAAATTGAA‑TTTTTTCACTCACTATTTTATTTTTAAAAAAcaacaa                                 <  1:616927/76‑1 (MQ=255)
                                  aCTACGAGGAAGGGAACAACATTCATACTGAAATTGAA‑TTTTTTCACTCACTATTTTATTTTTAAAAAACAACAAt                                <  2:230181/76‑1 (MQ=255)
                                  aCTACGAGGAAGGGAACAACATTCATACTGAAATTGAA‑TTTTTTCACTCACTATTTTATTTATAAAAAACAACAAt                                <  1:984269/76‑1 (MQ=255)
                                   cTACGAGGAAGGGAACAACATTCATACTGAAATTGAATTTTTTTCACTCACTATTTTATTTTTAAAAAACAACAAt                                >  2:1374034/1‑76 (MQ=255)
                                   cTACGAGGAAGGGAACAACATTCATACTGAAATTGAA‑TTTTTTCACTCACTATTTTATTTTTAAAAAACAACAAtt                               >  2:1217499/1‑76 (MQ=255)
                                    tACGAGGAAGGGAACAACATTCATACTGAAATTGAA‑TTTTTTCACTCACTATTTTATTTTTAAAAAACAACAAttt                              >  2:971160/1‑76 (MQ=255)
                                    tACGAGGAAGGGAACAACATTCATACTGAAATTGAA‑TTTTTTCACTCACTATTTTATTTTTAAAAAACAACAAttt                              >  1:516228/1‑76 (MQ=255)
                                     aCGAGGAAGGGAACAACATTCATACTGAAATTGAA‑TTTTTTCACTCACTATTTTATTTTTAAAAAACAACAATTta                             >  2:1010521/1‑76 (MQ=255)
                                     aCGAGGAAGGGAACAACATTCATACTGAAATTGAA‑TTTTTTCACTCACTATTTTATTTTTAAAAAACAACAATTta                             <  2:570548/76‑1 (MQ=255)
                                     aCGAGGAAGGGAACAACATTCATACTGAAATTGAA‑TTTTTTCACTCACTATTTTATTTTTAAAAAACAACAATTta                             <  1:209706/76‑1 (MQ=255)
                                     aCGAGGAAGGGAACAACATTCATACTGAAATTGAA‑TTTTTTCACTCACTATTTTACTTTTAAAAAACAACAAttca                             >  1:1365839/1‑74 (MQ=255)
                                      cGAGGAAGGGAACAACATTCATACTGAAATTGAA‑TTTTTTCACTCACTATTTTATTTTTAAAAAACAACAATTtat                            >  1:1150560/1‑76 (MQ=255)
                                       gAGGAAGGGAACAACATTCATACTGAAATTGAATTTTTTTCACTCACTATTTTATTTTTAAAAAACAACAATTtat                            <  2:485881/76‑1 (MQ=255)
                                       gAGGAAGGGAACAACATTCATACTGAAATTGAA‑TTTTTTCACTCACTATTTTATTTTTAAAAAACAACAATTtata                           >  2:837102/1‑76 (MQ=255)
                                        aGGAAGGGAACAACATTCATACTGAAATTGAA‑TTTTTTCACTCACTATTTTATTTTTAAAAAACAACAATTTatat                          >  2:260498/1‑76 (MQ=255)
                                        aGGAAGGGAACAACATTCATACTGAAATTGAA‑TTTTTTCACTCACTATTTTATTTTTAAAAAACAACAATTTatat                          <  1:1331779/76‑1 (MQ=255)
                                        aGGAAGGGAACAACATTCATACTGAAATTGAA‑TTTTTTCACTCACTATTTTATTTTTAAAAAACAACAATTTatat                          <  1:817918/76‑1 (MQ=255)
                                          gAAGGGAACAACATTCATACTGAAATTGAATTTTTTTCACTCACTATTTTATTTTTAAAAAACAACAATTTATAtt                         <  2:20868/76‑1 (MQ=255)
                                          gAAGGGAACAACATTCATACTGAAATTGAA‑TTTTTTCACTCACTATTTTATTTTTAAAAAACAACAATTTATATTg                        <  1:1616489/76‑1 (MQ=255)
                                          gAAGGGAACAACATTCATACTGAAATTGAA‑TTTTTTCACTCACTATTTTATTTTTAAAAAACAACAATTTATATTg                        <  1:226388/76‑1 (MQ=255)
                                           aaGGGAACAACATTCATACTGAAATTGAATTTTTTTCACTCACTATTTTATTTTTAAAAAACAACAATTTATATTg                        >  1:1194628/1‑76 (MQ=255)
                                           aaGGGAACAACATTCATACTGAAATTGAA‑TTTTTTCACTCACTATTTTATTTTTAAAAAACAACAATTTATATTGa                       >  1:1584091/1‑76 (MQ=255)
                                           aaGGGAACAACATTCATACTGAAATTGAA‑TTTTTTCACTCACTATTTTATTTTTAAAAAACAACAATTTATATTGa                       >  2:1103085/1‑76 (MQ=255)
                                           aaGGGAACAACATTCATACTGAAATTGAA‑TTTTTTCACTCACTATTTTATTTTTAAAAAACAACAATTTATATTGa                       <  1:1691785/76‑1 (MQ=255)
                                            aGGGAACAACATTCATACTGAAATTGAA‑TTTTTTCACTCACTATTTTATTTTTAAAAAACAACAATTTATATTGaa                      >  2:1265675/1‑76 (MQ=255)
                                            aGGGAACAACATTCATACTGAAATTGAA‑TTTTTTCACTCACTATTTTATTTTTAAAAAACAACAATTTATATTGaa                      <  1:319967/76‑1 (MQ=255)
                                            aGGGAACAACATTCATACTGAAATTGAA‑TTTTTTCACTCACTATTTTATTTTTAAAAAACAACAATTTATATTGaa                      >  1:378848/1‑76 (MQ=255)
                                               gAACAACATTCATACTGAAATTGAA‑TTTTTTCACTCACTATTTTATTTTTAAAAAACAACAATTTATATTGAAatt                   >  2:1539448/1‑76 (MQ=255)
                                                aacaacATTCATACTGAAATTGAA‑TTTTTTCACTCACTATTTTATTTTTAAAAAACAACAATTTATATTGAAatta                  <  1:1493756/76‑1 (MQ=255)
                                                aacaacATTCATACTGAAATTGAA‑TTTTTTCACTCACTATTTTATTTTTAAAAAACAACAATTTATATTGAAatta                  <  2:1458080/76‑1 (MQ=255)
                                                 acaacaTTCATACTGAAATTGAATTTTTTTCACTCTCTATTTTATTTTTAAAAAACAACAATTTATATTGAAatta                  <  2:531813/76‑1 (MQ=255)
                                                  caacaTTCATACTGAAATTGAA‑TTTTTTCACTCACTATTTTATTTTTAAAAAACAACAATTTATATTGAAattatt                >  2:440142/1‑76 (MQ=255)
                                                  caacaTTCATACTGAAATTGAA‑TTTTTTCACTCACTATTTAATTTTTAAAAAACAACAATTTATATTGAAattatt                <  2:565141/76‑1 (MQ=255)
                                                     caTTCATACTGAAATTGAA‑TTTTTTCACTCACTATTTTATTTTTAAAAAACAACAATTTATATTGAAATTATTaaa             <  1:1131699/76‑1 (MQ=255)
                                                      aTTCATACTGAAATTGAA‑TTTTTTCACTCACTATTTTATTTTTAAAAAACAACAATTTATATTGAAATTATTAAAc            >  1:489228/1‑76 (MQ=255)
                                                       ttCATACTGAAATTGAA‑TTTTTTCACTCACTATTTTATTTTTAAAAAACAACAATTTATATTGAAATTATTAAACg           <  1:418169/76‑1 (MQ=255)
                                                        tCATACTGAAATTGAATTTTTTTCACTCACTATTTTATTTTTAAAAAACAACAATTTATATTGAAATTATTAAACg           <  1:1291590/76‑1 (MQ=255)
                                                         cATACTGAAATTGAA‑TTTTTTCACTCACTATTTTATTTTTAAAAAACAACAATTTATATTGAAATTATTAAACGca         >  2:1759067/1‑76 (MQ=255)
                                                         cATACTGAAATTGAA‑TTTTTTCACTCACTATTTTATTTTTAAAAAACAACAATTTATATTGAAATTATTAAACGca         <  2:1083770/76‑1 (MQ=255)
                                                         cATACTGAAATTGAA‑TTTTTTCACTCACTATTTTATTTTTAAAAAACAACAATTTATATTGAAATTATTAAACGca         >  2:1250923/1‑76 (MQ=255)
                                                           tACTGAAATTGAA‑TTTTTTCACTCACTATTTTATTTTTAAAAAACAACAATTTATATTGAAATTATTAAACGcatc       <  1:1153701/76‑1 (MQ=255)
                                                              tGAAATTGAA‑TTTTTTCACTCACTATTTTATTTTTAAAAAACAACAATTTATATTGAAATTATTAAACGcatcatn    <  1:157868/76‑2 (MQ=255)
                                                              tGAAATTGAA‑TTTTTTCACTCACTATTTTATTTTTAAAAAACAACAATTTATATTGAAATTATTAAACGCATCATa    >  1:69779/1‑76 (MQ=255)
                                                              tGAAATTGAA‑TTTTTTCACTCACTATTTTATTTTTAAAAAACAACAATTTATATTGAAATTATTAAACGCATCATa    <  2:436812/76‑1 (MQ=255)
                                                               gAAATTGAA‑TTTTTTCACTCACTATTTTATTTTTAAAAAACAACAATTTATATTGAAATTATTAAACGCATCATaa   >  1:445097/1‑76 (MQ=255)
                                                               gAAATTGAA‑TTTTTTCACTCACTATTTTATTTTTAAAAAACAACAATTTATATTGAAATTATTAAACGCATCATaa   >  2:613456/1‑76 (MQ=255)
                                                               gAAATTGAA‑TTTTTTCACTCACTATTTTATTTTTAAAAAACAACAATTTATATTGAAATTATTAAACGCATCATaa   <  2:931713/76‑1 (MQ=255)
                                                                aaaTTGAA‑TTTTTTCACTCACTATTTTATTTTTAAAAAACAACAATTTATATTGAAATTATTAAACGCATCATaaa  >  1:1155142/1‑76 (MQ=255)
                                                                aaaTTGAA‑TTTTTTCACTCACTATTTTATTTTTAAAAAACAACAATTTATATTGAAATTATTAAACGCATCATaaa  <  1:1776332/76‑1 (MQ=255)
                                                                aaaTTGAA‑TTTTTTCACTCACTATTTTATTTTTAAAAAACAACAATTTATATTGAAATTATTAAACGCATCATaaa  <  1:387302/76‑1 (MQ=255)
                                                                        |                                                                    
TGATGCTCGCAAAAATGCAGCGGACAAAGGATGAACTACGAGGAAGGGAACAACATTCATACTGAAATTGAATTTTTTTCACTCACTATTTTATTTTTAAAAAACAACAATTTATATTGAAATTATTAAACGCATCATAAA  >  REL606/3911894‑3912034

Alignment Legend
Aligned base mismatch/match (shaded by quality score): ATCG/ATCG < 3 ≤ ATCG/ATCG < 25 ≤ ATCG/ATCG < 30 ≤ ATCG/ATCG < 35 ≤ ATCG/ATCG < 38 ≤ ATCG/ATCG
Unaligned base: atcg    Masked matching base: atcg    Alignment gap: ‑    Deleted base: ‑

GATK/CNVnator alignment

N/A