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 F17 I0 R1 87 56.5 4283937 98.6% 4223961 62.0

Breseq alignment

BRESEQ :: Evidence
Predicted mutation
evidence seq id position mutation freq annotation gene description
RA W3110S.gb 4,350,232 G→A 8.3% R3C (CGC→TGC)  yjdF ← conserved inner membrane protein

Read alignment evidence...
  seq id position ref new freq score (cons/poly) reads annotation genes product
*W3110S.gb4,350,2320GA 8.3% 264.2 / 10.9 84R3C (CGC→TGC) yjdFconserved inner membrane protein
Reads supporting (aligned to +/- strand):  ref base G (37/40);  new base A (2/5);  total (39/45)
Fisher's exact test for biased strand distribution p-value = 4.42e-01
Kolmogorov-Smirnov test that lower quality scores support variant p-value = 9.98e-01

GCCGGTATAAATCAGGATTAACGTTAGCGTCAGTGCGCTGGTGTTAAGAATTAACGGCTTGAGTGTGCGGGTCATGGTGAGTTCGCAAATCAGGGAAAATACTGACTATTCACCAGCAAGCGTGAAATTACAATCGCAA  >  W3110S.gb/4350164‑4350302
                                                                    |                                                                      
gCCGGTATAAATCAGGATTAACGTTAGCGTCAGTGCGCTGGTGTTAAGAATTAACGGCTTGAGTGTGCggg                                                                      >  1:1056418/1‑71 (MQ=255)
gCCGGTATAAATCAGGATTAACGTTAGCGTCAGTGCGCTGGTGTTAAGAATTAACGGCTTGAGTGTGCggg                                                                      >  1:2794135/1‑71 (MQ=255)
 ccGGTATAAATCAGGATTAACGTTAGCGTCAGTGCGCTGGTGTTAAGAATTAACGGCTTGAGTGTGCGGGt                                                                     <  1:2945974/71‑1 (MQ=255)
 ccGGTATAAATCAGGATTAACGTTAGCGTCAGTGCGCTGGTGTTAAGAATTAACGGCTTGAGTGTGCGGGt                                                                     <  1:1139910/71‑1 (MQ=255)
   ggTATAAATCAGGATTAACGTTAGCGTCAGTGCGCTGGTGTTAAGAATTAACGGCTTGAGTGTGCGGGTCa                                                                   <  1:1602975/71‑1 (MQ=255)
    gTATAAATCAGGATTAACGTTAGCGTCAGTGCGCTGGTGTTAAGAATTAACGGCTTGAGTGTGCGGGTCAt                                                                  <  1:1955677/71‑1 (MQ=255)
    gTATAAATCAGGATTAACGTTAGCGTCAGTGCGCTGGTGTTAAGAATTAACGGCTTGAGTGTGCGGGTCAt                                                                  >  1:3755110/1‑71 (MQ=255)
     tataAATCAGGATTAACGTTAGCGTCAGTGCGCTGGTGTTAAGAATTAACGGCTTGAGTGTGCGGGTCATg                                                                 <  1:3343013/71‑1 (MQ=255)
     tataAATCAGGATTAACGTTAGCGTCAGTGCGCTGGTGTTAAGAATTAACGGCTTGAGTGTGCGGGTCATg                                                                 <  1:2153073/71‑1 (MQ=255)
      ataAATCAGGATTAACGTTAGCGTCAGTGCGCTGGTGTTAAGAATTAACGGCTTGAGTGTGCGGGTCATgg                                                                >  1:31853/1‑71 (MQ=255)
      ataAATCAGGATTAACGTTAGCGTCAGTGCGCTGGTGTTAAGAATTAACGGCTTGAGTGTGCGGGTCATgg                                                                >  1:3808426/1‑71 (MQ=255)
      ataAATCAGGATTAACGTTAGCGTCAGTGCGCTGGTGTTAAGAATTAACGGCTAGAGTGTGCGGGTCATgg                                                                >  1:1459565/1‑71 (MQ=255)
       taAATCAGGATTAACGTTAGCGTCAGTGCGCTGGTGTTAAGAATTAACGGCTTGAGTGTGCGGGTCATgg                                                                <  1:1332496/70‑1 (MQ=255)
       taAATCAGGATTAACGTTAGCGTCAGTGCGCTGGTGTTAAGAATTAACGGCTTGAGTGTGCGGGTCATGGt                                                               >  1:3175238/1‑71 (MQ=255)
       taAATCAGGATTAACGTTAGCGTCAGTGCGCTGGTGTTAAGAATTAACGGCTTGAGTGTGCGGGTCATGGt                                                               >  1:3717649/1‑71 (MQ=255)
          aTCAGGATTAACGTTAGCGTCAGTGCGCTGGTGTTAAGAATTAACGGCTTGAGTGTGCGGGTCATGGTGAg                                                            >  1:1634589/1‑71 (MQ=255)
             aGGATTAACGTTAGCGTCAGTGCGCTGGTGTTAAGAATTAACGGCTTGAGTGTGCGGGTCATGGTGAGTTc                                                         >  1:1352217/1‑71 (MQ=255)
             aGGATTAACGTTAGCGTCAGTGCGCTGGTGTTAAGAATTAACGGCTTGAGTGTGCGGGTCATGGTGAGTTc                                                         >  1:1623211/1‑71 (MQ=255)
                aTTAACGTTAGCGTCAGTGCGCTGGTGTTAAGAATTAACGGCTTGAGTGTGCGGGTCATGGTGAGTTCGCa                                                      <  1:3176751/71‑1 (MQ=255)
                 ttAACGTTAGCGTCAGTGCGCTGGTGTTAAGAATTAACGGCTTGAGTGTGCGGGTCATGGTGAGTTCGCa                                                      >  1:1844925/1‑70 (MQ=255)
                 ttAACGTTAGCGTCAGTGCGCTGGTGTTAAGAATTAACGGCTTGAGTGTGCGGGTCATGGTGAGTTCGCa                                                      >  1:1097770/1‑70 (MQ=255)
                 ttAACGTTAGCGTCAGTGCGCTGGTGTTAAGAATTAACGGCTTGAGTGTGCGGGTCATGGTGAGTTCGCa                                                      >  1:4201826/1‑70 (MQ=255)
                   aaCGTTAGCGTCAGTGCGCTGGTGTTAAGAATTTACGGCTTGAGTGTGCGGGTCATGGTGAGTTCGCaaa                                                    >  1:4128427/1‑70 (MQ=255)
                    aCGTTAGCGTCAGTGCGCTGGTGTTAAGAATTAACGGCTTGAGTGTGCGGTTCATGGTGAGTTCGCAAATc                                                  <  1:3654980/71‑1 (MQ=255)
                    aCGTTAGCGTCAGTGCGCTGGTGTTAAGAATTAACGGCTTGAGTGTGCGGGTCATGGTGAGTTCGCAAAt                                                   >  1:3390186/1‑70 (MQ=255)
                    aCGTTAGCGTCAGTGCGCTGGTGTTAAGAATTAACGGCTTGAGTGTGCGGGTCATGGTGAGTTCGCAAATc                                                  <  1:903940/71‑1 (MQ=255)
                    aCGTTAGCGTCAGTGCGCTGGTGTTAAGAATTAACGGCTTGAGTGTGCGGGTCATGGTGAGTTCGCAAATc                                                  <  1:917618/71‑1 (MQ=255)
                    aCGTTAGCGTCAGTGCGCTGGTGTTAAGAATTAACGGCTTGAGTGTGCGGGTCATGGTGAGTTCGCAAATc                                                  <  1:1099072/71‑1 (MQ=255)
                     cGTTAGCGTCAGTGCGCTGGTGTTAAGAATTAACGGCTTGAGTGTGCGGGTCATGGGGAGTTCGCAAATCa                                                 <  1:3526082/71‑1 (MQ=255)
                       ttAGCGTCAGTGCGCTGGTGTTAAGAATTAACGGCTTGAGTGTGCGGGTCATGGTg                                                              <  1:3684426/56‑1 (MQ=255)
                       ttAGCGTCAGTGCGCTGGTGTTAAGAATTAACGGCTTGAGTGTGCAGGTCATGGTGAGTTCGCAAATCAgg                                               <  1:421055/71‑1 (MQ=255)
                         aGCGTCAGTGCGCTGGTTTTAAGAATTAACGGCTTGAGTGTGCgg                                                                       >  1:984672/1‑45 (MQ=255)
                         aGCGTCAGTGCGCTGGTGTTAAGAATTAACGGCTTGAGTGTGCGGGTCATGGTGAGTTCGCAAATCAggg                                              >  1:3563271/1‑70 (MQ=255)
                           cGTCAGTGCGCTGGTGTTAAGAATTAACGGCTTGAGTGTGCGGGTCATGGTGAGTTCGCAAATCAGGGaaa                                           <  1:1643261/71‑1 (MQ=255)
                             tCAGTGCGCTGGTGTTAAGAATTAACGGCTTGAGTGTGCGGGTCATGGTGAGTTCGCAAATCa                                                 <  1:1859551/63‑1 (MQ=255)
                             tCAGTGCGCTGGTGTTAAGAATTAACGGCTTGAGTGTGCGGGTCATGGTGAGTTCGCAAATCa                                                 <  1:2272811/63‑1 (MQ=255)
                             tCAGTGCGCTGGTGTTAAGAATTAACGGCTTGAGTGTGCAGGTCATGGTg                                                              <  1:2370305/50‑1 (MQ=255)
                               aGTGCGCTGGTGTTAAGAATTAACGGCTTGAGTGTGCGGGTCATGGTGAGTTCGCAAATCAGGGAAAATa                                        <  1:1834888/70‑1 (MQ=255)
                               aGTGCGCTGGTGTTAAGAATTAACGGCTTGAGTGTGCGGGTCATGGTGAGTTCGCAAATCAGGGAAAATa                                        <  1:1829954/70‑1 (MQ=255)
                               aGTGCGCTGGTGTTAAGAATTAACGGCTTGAGTGTGCGGGTCATGGTGAGTTCGCAAATCAGGGAAAATAc                                       >  1:616297/1‑71 (MQ=255)
                                gTGCGCTGGTGTTAAGAATTAACGGCTTGAGTGTGCGGGTCATGGTGAGTTCGCAAATCAGGGAAAATACt                                      <  1:2046729/71‑1 (MQ=255)
                                gTGCGCTGGTGTTAAGAATTAACGGCTTGAGTGTGCGGGTCATGGTGAGTTCGCAAATCAGGGAAAATACt                                      <  1:2684309/71‑1 (MQ=255)
                                 tGCGCTGGTGTTAAGAATTAACGGCTTGAGTGTGCGGGTCATGGTGAGTTCGCaa                                                     <  1:3023066/55‑1 (MQ=255)
                                 tGCGCTGGTGTTAAGAATTAACGGCTTGAGTGTGCGGGTCATGGTGAGTTCGCa                                                      <  1:947986/54‑1 (MQ=255)
                                   cgcTGGTGTTAAGAATTAACGGCTTGAGTGTGCGGGTCATGGt                                                               >  1:2680651/1‑43 (MQ=255)
                                   cgcTGGTGTTAAGAATTAACGGCTTGAGTGTGCGGGTCATGGTGAGt                                                           >  1:104243/1‑47 (MQ=255)
                                   cgcTGGTGTTAAGAATTAACGGCTTGAGTGTGCGGGTCATGGTGAGTTCGc                                                       >  1:3032135/1‑51 (MQ=255)
                                   cgcTGGTGTTAAGAATTAACGGCTTGAGTGTGCGGGTCATGGTGAGTTCGc                                                       >  1:1715073/1‑51 (MQ=255)
                                   cgcTGGTGTTAAGAATTAACGGCTTGAGTGTGCAGGTCATGGTGAGTTCGCAAATCa                                                 >  1:1985538/1‑57 (MQ=255)
                                       ggTGTTAAGAATTAACGGCTTGAGTGTGCAGGTCATGGTGAGTTCGCAAATCAgg                                               <  1:829892/55‑1 (MQ=255)
                                        gtgtTAAGAATTAACGGCTTGAGTGTGCGGGTCATGGTGAGTTCGCAAAt                                                   >  1:1918868/1‑50 (MQ=255)
                                        gtgtTAAGAATTAACGGCTTGAGTGTGCGGGTCATGGTGAGTTCGCAAAt                                                   >  1:4033205/1‑50 (MQ=255)
                                        gtgtTAAGAATTAACGGCTTGAGTGTGCGGGTCATGGTGAGTTCGCAAATCAGGGAAAATACTGACTAt                                <  1:1683399/69‑1 (MQ=255)
                                           ttAAGAATTAACGGCTTGAGTGTGCGGGTCATGGt                                                               <  1:1144459/35‑1 (MQ=255)
                                           ttAAGAATTAACGGCTTGAGTGTGCGGGTCATGGt                                                               <  1:4247127/35‑1 (MQ=255)
                                           ttAAGAATTAACGGCTTGAGTGTGCGGGTCATGGTGAGTTCGCAAATCAGGGAAAATACTGACTATTCAc                            <  1:3597072/70‑1 (MQ=255)
                                             aaGAATTAACGGCTTGAGTGTGCGGGTCATGGTGAGTTCGCAAATCAGGGAAAATACTGACTATTCACCAg                         >  1:619899/1‑71 (MQ=255)
                                             aaGAATTAACGGCTTGAGTGTGCGGCTCATGGTGAGTTCGCAAATCAGGGAAAATACTGACTATTCACCAg                         >  1:3233506/1‑71 (MQ=255)
                                              aGAATTAACGGCTTGAGTGTGCGTGTCATGGTGAGTTCGCAAAt                                                   <  1:4194332/44‑1 (MQ=255)
                                               gAATTATCGGCTTGAGTGTGCAGGTCATGGTGAGTTCGCAAATCAGGGaaa                                           >  1:549717/1‑51 (MQ=255)
                                                aaTTAACGGCTTGAGTGTGCGGGTCATGGTGAGtt                                                          >  1:360019/1‑35 (MQ=255)
                                                  ttAACGGCTTGAGTGTGCGGGTCATGGTGAGTTCGCAAATCAGGGa                                             <  1:1992224/46‑1 (MQ=255)
                                                  ttAACGGCTTGAGTGTGCGGGTCATGGTGAGTTCGCAAATCAGGGAAAATACTGACTATTCACCAGCAAGc                    >  1:3314187/1‑71 (MQ=255)
                                                  ttAACGGCTTGAGTGTGCAGGTCATGGTGAGTTCGCAAATCAGGGaa                                            <  1:2019/47‑1 (MQ=255)
                                                  ttAACGGCTTGAGTGTGCAGGTCATGGTGAGTTCGCAAATCAGGGaa                                            <  1:3201151/47‑1 (MQ=255)
                                                    aaCGGCTTGAGTGTGCGGGTCATGGTGAGTTCGCa                                                      <  1:653420/35‑1 (MQ=255)
                                                    aaCGGCTTGAGTGTGCGGGTCATGGTGAGTTCGCAAATCAGGGaa                                            >  1:1513997/1‑45 (MQ=255)
                                                     aCGGCTTGAGTGTGCGGGTCATGGTGAGTTCGCAAATCAGGGAAAATa                                        >  1:1089992/1‑48 (MQ=255)
                                                     aCGGCTTGAGTGTGCGGGTCATGGTGAGTTCGCAAATCAGGGAAAATACTGACTATTCACCAGCAAGCGTg                 <  1:4272278/71‑1 (MQ=255)
                                                      cGGCTTGAGTGTGCGGGTCATGGTGAGTTCGCAAATCAGGGaa                                            <  1:3821694/43‑1 (MQ=255)
                                                      cGGCTTGAGTGTGCGGGTCATGGTGAGTTCGCAAATCAGGGAAAATACTGACTATTCACCAGCAAGCGt                  >  1:3028489/1‑69 (MQ=255)
                                                      cGGCTTGAGTGTGCGGGTCATGGTGAGTTCGCAAATCAGGGAAAATACTGACTATTCACCAGCAAGCGt                  <  1:2931128/69‑1 (MQ=255)
                                                      cGGCTTGAGTGTGCGGGTCATGGTGAGTTCGCAAATCAGGGAAAATACTGACTATTCACCAGCAAGCGTg                 >  1:3310207/1‑70 (MQ=255)
                                                       ggCTTGAGTGTGCGGGTCATGGTGAGTTCGCAAATCAGGGaa                                            <  1:4195416/42‑1 (MQ=255)
                                                       ggCTTGAGTGTGCGGGTCATGGTGAGTTCGCAAATCAGGGAAAATACTGACTATTCACCAGCAAGCGTGaa               <  1:3807039/71‑1 (MQ=255)
                                                        gCTTGAGTGTGCGGGTCATGGTGAGTTCGCAAATCAGGGAAAATACTGACTATTCACCAGCAAGCGTGaaa              >  1:4004292/1‑71 (MQ=255)
                                                        gCTTGAGTGTGCGGGTCATGGTGAGTTCGCAAATCAGGGAAAATACTGACTATTCACCAGCAAGCGTGaa               >  1:571234/1‑70 (MQ=255)
                                                         cTTAAGTGTGCGGGTCATGGTGAGTTCGCAAATCAGGGAAAATACTGACTATTCACCAGc                        <  1:3072867/60‑1 (MQ=255)
                                                            gAGTGTGCGGGTCATGGTGAGTTCGCAAATCAGGGAAAATa                                        <  1:3728367/41‑1 (MQ=255)
                                                            gAGTGTGCGGGTCATGGTGAGTTCGCAAATCAGGGAAAATACTGACTATTCACCAGCAAGCGTGAAATTa           >  1:3095298/1‑70 (MQ=255)
                                                             aGTGTGCGGGTCATGGTGAGTTCGCAAATCAGGGAAAATACTGACTATTCACCAGCAAGCGTGAAATTAc          <  1:1533116/70‑1 (MQ=255)
                                                              gtgtGCGGGTCATGGTGAGTTCGCAAATCAGGGAAAATACTGACTATTCACCAGCAAGCGTGAAATTACaa        <  1:4665/71‑1 (MQ=255)
                                                              gtgtGCGGGTCATGGTGAGTTCGCAAATCAGGGAAAATACTGACTATTCACCAGCAAGCGTGAAATTACaa        >  1:3531000/1‑71 (MQ=255)
                                                               tgtgCGGGTCATGGTGAGTTCGCAAATCAGGGAAAATACTGACTATTCACCAg                         <  1:706294/53‑1 (MQ=255)
                                                                gtgCGGGTCATGGTGAGTTCGCAAATCAGGGAAAATACTGACTATTCACCAGCAAGCGTGaaa              >  1:1411977/1‑63 (MQ=255)
                                                                gtgCGGGTCATGGTGAGTTCGCAAATCAGGGAAAATACTGACTATTCACCAGCAAGCGTGaaa              >  1:3152833/1‑63 (MQ=255)
                                                                   cGGGTCATGGTGAGTTCGCAAATCAGGGAAAATACTGACTATTCACCAGCAAGCGTGAAATTACAATCg     >  1:652606/1‑69 (MQ=255)
                                                                    gggTCATGGTGAGTTCGCAAATCAGGGAAAATACTGACTATTCACCAGCAAGCGTGAAATTACAATCGCaa  <  1:39758/71‑1 (MQ=255)
                                                                    |                                                                      
GCCGGTATAAATCAGGATTAACGTTAGCGTCAGTGCGCTGGTGTTAAGAATTAACGGCTTGAGTGTGCGGGTCATGGTGAGTTCGCAAATCAGGGAAAATACTGACTATTCACCAGCAAGCGTGAAATTACAATCGCAA  >  W3110S.gb/4350164‑4350302

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