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
A6 F21 I0 R1 2169 63.0 3952800 76.2% 3012033 62.4

Breseq alignment

BRESEQ :: Evidence
Predicted mutation
evidence seq id position mutation freq annotation gene description
RA minE 1,439,333 A→C 11.9% A323A (GCT→GCG)  ompC ← outer membrane porin protein C

Read alignment evidence...
  seq id position ref new freq score (cons/poly) reads annotation genes product
*minE1,439,3330AC11.9% 262.6 / 31.2 109A323A (GCT→GCG) ompCouter membrane porin protein C
Reads supporting (aligned to +/- strand):  ref base A (54/42);  new base C (7/6);  total (61/48)
Fisher's exact test for biased strand distribution p-value = 1.00e+00
Kolmogorov-Smirnov test that lower quality scores support variant p-value = 9.90e-01

Only 100 of 133 total aligned reads displayed.

CTGGTTGTCGTCCAGCAGGTTGATTTTGTAGTCAACGTAGGTGGACATGTTTTTGTTGAAGTAGTAGGTAGCACCAACATCAACATATTTCAGGATATCTTCGTCGTCGTAGCCACGACCCAGGTTTTTACCTTTAGAC  >  minE/1439264‑1439402
                                                                     |                                                                     
cTGGTTGTCGTCCAGCAGGTTGATTTTGTAGTCAACGTAGGTGGACATGTTTTTGTTGAAGTAgtaggtag                                                                      >  1:3845183/1‑71 (MQ=255)
cTGGTTGTCGTCCAGCAGGTTGATTTTGTAGTCAACGTAGGTGGACATGTTTTTGTTGAAGTAgtaggtag                                                                      <  1:1321057/71‑1 (MQ=255)
   gTTGTCGTCCAGCAGGTTGACTTTGTAGTCAACGTAGGTGGACATGTTTTTGTTGAAGTAgtaggtag                                                                      <  1:1325754/68‑1 (MQ=255)
     tGTCGTCCAGCAGGTTGATTTTGTAGTCAACGTAGGTGGACATGTTTTTGTTGAAGTAGTAGGTAGCAcc                                                                  >  1:2268900/1‑70 (MQ=255)
     tGTCGTCCAGCAGGTTGATTTTGTAGTCAACGTAGGTGGACATGTTTTTGTTGAAGTAGTAGGTAGCAcc                                                                  >  1:2228426/1‑70 (MQ=255)
      gtcgtcCAGCAGGTTGATTTTGTAGTCAACGTAGGTGGACATGTTTTTGTTGAAGTAGTAGGTAGCACcaa                                                                >  1:1739682/1‑71 (MQ=255)
        tgtcCAGCAGGTTGATTTTGTAATCAACATAGGTGGACATGTTTTTGTTGAAGTAGTAGGTCGCACcaat                                                               >  1:607587/2‑69 (MQ=18)
         gtcCAGCAGGTTGATTTTGTAGTCAACGTAGGTGGACATGTTTTTGTTGAAGTAGTAGGTAGCACcaacat                                                             >  1:2144461/1‑71 (MQ=255)
         gtcCAGCAGGTTGATTTTGTAGTCAACGTAGGTGGACATGTTTTTGTTGAAGTAGTAGGTAGCACcaaca                                                              <  1:1061213/70‑1 (MQ=255)
         gtcCAGCAGGTTGATTTTGTAGTCAACGTAGGTGGACATGTTTTTGTTGAAGTAGTAGGTAGCACcaa                                                                >  1:2533968/1‑68 (MQ=255)
         gtcCAGCAGGTTGATTTTGTAGTCAACGTAGGTGGACATGTTTTTGTTGAAGTAGTAGGTAGCACcaa                                                                >  1:2760528/1‑68 (MQ=255)
         gtcCAGCAGGTTGATTTTGTAGTCAACGTAGGTGGACATGTTTTTGTTGAAGTAGTAGGTAGCACcaa                                                                >  1:1693408/1‑68 (MQ=255)
          tcCAGCAGGTTGATTTTGTAGTCAACGTAGGTGGACATGTTTTTGTTGAAGTAGTAGGTAGCACca                                                                 <  1:1011954/66‑1 (MQ=255)
          tcCAACAGGTTGATTTTATAGTCAACGTAGGTGGACATGTTTTTATTGAAATAGTAAGTCGCGCcaatatc                                                            <  1:2961234/71‑1 (MQ=17)
           ccAGCAGGTTGATTTTGTAATCAACATAGGTGGACATGTTTTTGTTGAAGTAGTAGGTCGCAc                                                                   >  1:2487385/1‑63 (MQ=17)
            cagcagGTTGATTTTGTAGTCAACGTAGGTGGACATGTTTTTGTTGAAGTAGTAGGTAGCACcaacatcaa                                                          >  1:1212347/1‑71 (MQ=255)
            cagcagGTTGATTTTGTAGTCAACGTAGGTGGACATGTTTTTGTTGAAGTAGTAGGTAGCACcaacatcaa                                                          <  1:3102972/71‑1 (MQ=255)
            cagcagGTTGATTTTGTAGTCAACGTAGGTGGACATGTTTTTGTTGAAGTAGTAGGTAGCACcaacatcaa                                                          >  1:228492/1‑71 (MQ=255)
            cagcagGTTGATTTTGTAGTCAACGTAGGTGGACATGTTTTTGTTGAAGTAGTAGGTAGCACcaacatca                                                           >  1:913247/1‑70 (MQ=255)
            cagcagGTTGATTTTGTAGTCAACGTAGGTGGACATGTTTTTGTTGAAGTAGTAGGTAGCACcaacatca                                                           <  1:610761/70‑1 (MQ=255)
            cagcagGTTGATTTTGTAGTCAACGTAGGTGGACATGTTTTTGTTGAAGTAGTAGGTAGCACcaac                                                               >  1:3914110/1‑66 (MQ=255)
                agGTTGATTTTGTAGTCAACGTAGGTGGACATGTTTTTGTTGAAGTAGTAGGTAGCACCAACATCAACata                                                      >  1:6731/1‑71 (MQ=255)
                agGTTGATTTTGTAATCAACATAGGTGGACATGTTTTTGTTGAAGTAGTAGGTCGCACCAATATCAACgta                                                      <  1:1427285/71‑1 (MQ=17)
                  gTTGATTTTGTAATCAACATAGGTGGACATGTTTTTGTTGAAGTAGTAGGTCGCACCAATATCAACGTAtt                                                    <  1:1979892/71‑1 (MQ=17)
                  gTTGATTTTGTAATCAACATAGGTGGACATGTTTTTGTTGAAGTAGTAGGTCGCACCAATATCAACGTAtt                                                    >  1:846419/1‑71 (MQ=17)
                   ttGATTTTGTAGTCAACGTAGGTGGACATGTTTTTGTTGAAGTAGTAGGTAGCACcaaca                                                              <  1:2850459/60‑1 (MQ=255)
                   ttGATTTTGTAGTCAACGTAGGTGGACATGTTTTTGTTGAAGTAGTAGGTAGCACCAACATCAACATAttt                                                   <  1:3649937/71‑1 (MQ=255)
                   ttGATTTTGTAATCAACATAGGTGGACATGTTTTTGTTGAAGTAGTAGGTCGCACCAATATCAACgtat                                                     <  1:1569583/69‑1 (MQ=17)
                    tGATTTTGTAGTCAACGTAGGTGGACATGTTTTTGTTGAAGTAGTAGTTAGCACCAACATCAACATAttt                                                   <  1:2196761/70‑1 (MQ=255)
                     gATTTTGTAGTCAACGTAGGTGGACATGTTTTTGTTGAAGTAGTAGGTAGCACCAACATCAACATAttt                                                   >  1:1403947/1‑69 (MQ=255)
                     gATTTTGTAATCAACATAGGTGGACATGTTTTTGTTGAAGTAGTAGGTCGCa                                                                    >  1:709239/1‑52 (MQ=11)
                      aTTTTGTAGTCAACGTAGGTGGACATGTTTTTGTTGAAGTAGTAGGTAGCACcaacatca                                                           <  1:1468494/60‑1 (MQ=255)
                      aTTTTGTAGTCAACGTAGGTGGACATGTTTTTGTTGAAGTAGTAGGTAGCACCAACATCAACATATTTCAg                                                >  1:337752/1‑71 (MQ=255)
                      aTTTTGTAGTCAACGTAGGTGGACATGTTTTTGTTGAAGTAGTAGGTAGCACCAACATCAACATATTTCAg                                                >  1:266866/1‑71 (MQ=255)
                      aTTTTGTAATCAACATAGGTGGACATGTTTTTGTTGAAGTAGTAGGTCGCACCAATATCAACGTAtttaac                                                >  1:2105972/1‑68 (MQ=17)
                         ttGTAGTCAACGTAGGTGGACATGTTTTTGTTGAAGTAGTAGGTAGCACCAACATCAACatat                                                     >  1:1383626/1‑63 (MQ=255)
                          tGTAGTCAACGTAGGTGGACATGTTTTTGTTGAAGTAgtaggtag                                                                      >  1:1222490/1‑45 (MQ=255)
                          tGTAGTCAACGTAGGTGGACATGTTTTTGTTGAAGTAgtaggtag                                                                      >  1:3366072/1‑45 (MQ=255)
                          tGTAGTCAACGTAGGTGGACATGTTTTTGTTGAAGTAGTAGGTAGCACCAACATCAACATATTTCAGGata                                            >  1:3830735/1‑71 (MQ=255)
                           gTAATCAACATAGGTGGACATGTTTTTGTTGAAGTAGTAGGTCGCACCAATATCAACGTAttta                                                  <  1:286979/64‑2 (MQ=14)
                                cAACGTAGGTGGACATGTTTTTGTTGAAGTAGTAGGTAGCACCAACATCAACATATTTCAGGATATCTtcg                                      >  1:2766091/1‑71 (MQ=255)
                                cAACGTAGGTGGACATGTTTTTGTTGAAGTAGTAGGTAGCACCAACATCAACATATTTCAGGATATCTtcg                                      >  1:3773224/1‑71 (MQ=255)
                                cAACGTAGGTGGACATGTTTTTGTTGAAGTAGTAGGTAGCACCAACATCAACATATTTCAGGATATCTtcg                                      >  1:913596/1‑71 (MQ=255)
                                 aaCGTAGGTGGACATGTTTTTGTTGAAGTAGTAGGTAGCACCAACATCAACATATTTCAGGATATCTtcgt                                     <  1:768937/71‑1 (MQ=255)
                                 aaCGTAGGTGGACATGTTTTTGTTGAAGTAGTAGGTAGCACCAACATCAACATATTTCAGGATATCTtcgt                                     >  1:1859737/1‑71 (MQ=255)
                                 aaCGTAGGTGGACATGTTTTTGTTGAAGTAGTAGGTAGCACCAACATCAACATATTTCAGGATATCTtcgt                                     >  1:3283224/1‑71 (MQ=255)
                                 aaCGTAGGTGGACATGTTTTTGTTGAAGTAGTAGGTAGCACCAACATCAACATATTTCAGGATATCTtcgt                                     >  1:84653/1‑71 (MQ=255)
                                 aaCGTAGGTGGACATGTTTTTGTTGAAGTAGTAGGTAGCACCAACATCAACATATTTCAGGATATCTtcgt                                     >  1:1490119/1‑71 (MQ=255)
                                 aaCGTAGGTGGACATGTTTTTGTTGAAGTAGTAGGTAGCACCAACATCAACATATTTCAGGATATCTtcgt                                     <  1:2426043/71‑1 (MQ=255)
                                  aCGTAGGTGGACATGTTTTTGTTGAAGTAGTAGGTAGCAcc                                                                  <  1:1273188/41‑1 (MQ=255)
                                  aCGTAGGTGGACATGTTTTTGTTGAAGTAGTAGGTAGCAcc                                                                  <  1:1398748/41‑1 (MQ=255)
                                  aCGTAGGTGGACATGTTTTTGTTGAAGTAGTAGGTAGCAcc                                                                  <  1:2177345/41‑1 (MQ=255)
                                   cGTAGGTGGACATGTTTTTGTTGAAGTAGTAGGTAGCACCAACATCAACATATTTCAGGATATCTtcgtcg                                   >  1:3309534/1‑71 (MQ=255)
                                   cGTAGGTGGACATGTTTTTGTTGAAGTAGTAGGTAGCACCAACATCAACATATTTCAGGATATCTtcgtcg                                   <  1:2936115/71‑1 (MQ=255)
                                    gTAGGTGGACATGTTTTTGTTGAAGTAGTAGGTAGCACcaacatcaaca                                                        <  1:3158368/49‑1 (MQ=255)
                                    gTAGGTGGACATGTTTTTGTTGAAGTAGTAGGTAGCACcaacatcaac                                                         >  1:1180375/1‑48 (MQ=255)
                                      aGGTGGACATGTTTTTGTTGAAGTAGTAGGTAGCACCAACATCAACATATTTCAg                                                >  1:1898993/1‑55 (MQ=255)
                                       ggTGGACATGTTTTTGTTGAAGTAGTAGGTAGCACCAACATCAACATATTTCAGGATATCTtcgtcgtcg                                <  1:1212962/70‑1 (MQ=255)
                                       ggTGGACATGTTTTTGTTGAAGTAGTAGGTAGCACCAACATCAACATATTTCAGGATATCTtcgtcgtcg                                <  1:2245513/70‑1 (MQ=255)
                                       ggTGGACATGTTTTTGTTGAAGTAGTAGGTAGCACCAACATCAACATATTTCAGGATATCTTcgtcgtcgt                               <  1:2067317/71‑1 (MQ=255)
                                         tGGACATGTTTTTGTTGAAGTAGTAGGTAGCACCAACATCAACATATTTCAGGATATCTTCGTCGTCGTAg                             <  1:677489/71‑1 (MQ=255)
                                          ggACATGTTTTTGTTGAAGTAGTAGGTAGCACCAACATCAACata                                                      <  1:2087906/45‑1 (MQ=255)
                                           gACATGTTTTTGTTGAAGTAGTAGGTAGCACCAACATCAACATATTTCAGGATATCTTCGTCGTCGTAGc                            <  1:831157/70‑1 (MQ=255)
                                             cATGTTTTTGTTGAAGTAGTAGGTAGCACcaacatcaa                                                          <  1:869980/38‑1 (MQ=255)
                                             cATGTTTTTGTTGAAGTAGTAGGTAGCACcaacatcaa                                                          <  1:1130934/38‑1 (MQ=255)
                                             cATGTTTTTGTTGAAGTAGTAGGTAGCACCAACATCAACATATTTCAg                                                <  1:3423951/48‑1 (MQ=255)
                                             cATGTTTTTGTTGAAGTAGTAGGTAGCACCAACATCAACATATTTCAGGATATCTTCGTCGTCGTAGCCAc                         >  1:2730546/1‑71 (MQ=255)
                                             cATGTTTTTGTTGAAGTAGTAGGTAGCACCAACATCAACATATTTCAGGATATCTTCGTCGTCGTAGCCAc                         >  1:744297/1‑71 (MQ=255)
                                              aTGTTTTTGTTGAAGTAGTAGGTAGCACCAACATCAACATATTTCa                                                 >  1:445309/1‑46 (MQ=255)
                                              aTGTTTTTGTTGAAGTAGTAGGTAGCACCAACATCAACATATTTCAGGATATc                                          <  1:2309932/53‑1 (MQ=255)
                                              aTGTTTTTGTTGAAGTAGTAGGTAGCACCAACATCAACATATTTCAGGATATCTTCGTCGTCGTAGCCAc                         <  1:1194254/70‑1 (MQ=255)
                                                gTTTTTGTTGAAGTAGTAGGTAGCACCAACATCAACATATTTCAGGATATCTTCGTCGTCGTAGCCACGAc                      >  1:1835107/1‑71 (MQ=255)
                                                  ttttGTTGAAGTAGTAGGTAGCACCAACATCAACATAttt                                                   >  1:1186247/1‑40 (MQ=255)
                                                   tttGTTGAAGTAGTAGGTAGCACCAACATCAACATATTTCAGGATATCTTCGTCGTCGTAGCCACGAccc                    <  1:113510/70‑1 (MQ=255)
                                                    ttgttgAAGTAGTAGGTAGCACCAACATCAACATATTTCAg                                                <  1:1564399/41‑1 (MQ=255)
                                                       ttgAAGTAGTAGGTAGCACCAACATCAACATATTTCAGGATATCTtcgtcgtc                                 <  1:2816240/53‑1 (MQ=255)
                                                       ttgAAGTAGTAGGTAGCACCAACATCAACATATTTCAGGATATCTtcg                                      <  1:400070/48‑1 (MQ=255)
                                                       ttgAAGTAGTAGGTAGCACCAACATCAACATATTTCAGGATATCTTCGTCGTCGTAGcc                           <  1:2650918/59‑1 (MQ=255)
                                                       ttgAAGTAGTAGGTAGCACCAACATCAACATATTTCAGGATATCTTCGTCGTCGTAGCCACGACCCAGGtt               <  1:1854039/71‑1 (MQ=255)
                                                        tgAAGTAGTAGGTAGCACCAACATCAACATATTTCAGGATATCTTCGTCGTCGTAGCCACGACCCa                   >  1:1464743/1‑66 (MQ=255)
                                                         gAAGTAGTAGGTAGCACCAACATCAACATATTTCAGGATATCTTCGTCGTCGTAGCCACGACCCAGGtttt             >  1:1663130/1‑71 (MQ=255)
                                                          aaGTAGTAGGTAGCACCAACATCAACATATTTCAGGATATCTtcgtc                                    >  1:2637825/1‑47 (MQ=255)
                                                           agtagtAGGTAGCACCAACATCAACATATTTCAgg                                               <  1:3137842/35‑1 (MQ=255)
                                                            gtagtaGGTAGCACCAACATCAACATATTTCAGGATATCt                                         <  1:1968252/40‑1 (MQ=255)
                                                            gtagtaGGTAGCACCAACATCAACATATTTCAGGATATCTTCGTCGTCGTAGCCACGACCCAGGTTTTTAc          >  1:1574488/1‑71 (MQ=255)
                                                              agtagGTAGCACCAACATCAACATATTTCAGGATATCTtc                                       >  1:1279508/1‑40 (MQ=255)
                                                              agtagGTAGCACCAACATCAACATATTTCAGGATATCTtc                                       >  1:458097/1‑40 (MQ=255)
                                                              agtagGTAGCACCAACATCAACATATTTCAGGATATCTtc                                       >  1:811461/1‑40 (MQ=255)
                                                               gtaggtagCACCAACATCAACATATTTCAGGATATCTTCGTCGTCGTAGCCACGACCCAGGTTTTTACCtt       <  1:32502/71‑1 (MQ=255)
                                                               gtaggtagCACCAACATCAACATATTTCAGGATATCTTCGTCGTCGTAGCCACGACCCAGGTTTTTACCt        <  1:561327/70‑1 (MQ=255)
                                                                taggtagCACCAACATCAACATATTTCAGGATATCTtcgtcgtc                                 <  1:2317429/44‑1 (MQ=255)
                                                                taggtagCACCAACATCAACATATTTCAGGATATCTTCGTCGTCGTAGCCACGACCCAGGTTTTTACCttt      <  1:759130/71‑1 (MQ=255)
                                                                 aggtagCACCAACATCAACATATTTCAGGATATCTtcgtcgtc                                 >  1:940575/1‑43 (MQ=255)
                                                                 aggtagCACCAACATCAACATATTTCAGGATATCTTCGTCGTCGTAGCCACGAcc                     <  1:305496/55‑1 (MQ=255)
                                                                 aggtagCACCAACATCAACATATTTCAGGATATCTTCGTCGTCGTAGCCACGACCCAGGTTTTTACCtt       >  1:1308363/1‑69 (MQ=255)
                                                                  ggtagCACCAACATCAACATATTTCAGGATATCTTCGTCGTCGTAGCCACGACCCAGGTTTTTACCTTTa     <  1:763259/70‑1 (MQ=255)
                                                                   gtagCACCAACATCAACATATTTCAGGATATCTTCGTCGTCGTAGCCACGACCCAGGTTTTTACCTTTAGa   >  1:2959950/1‑71 (MQ=255)
                                                                    tagCACCAACATCAACATATTTCAGGGTATCTTCGTCGTCGTAGCCACGACCCAGGTTTTTACCTTTAGAc  >  1:3182106/1‑71 (MQ=255)
                                                                     agCACCAACATCAACATATTTCAGGATATCTTCGTCGTCGTAGCCACGACCCAGGTTTTTACCttt      <  1:3234716/66‑1 (MQ=255)
                                                                     agCACCAACATCAACATATTTCAGGATATCTTCGTCGTCGTAGCCACGACCCAGGTTTTTACCTTTa     >  1:3640622/1‑67 (MQ=255)
                                                                     |                                                                     
CTGGTTGTCGTCCAGCAGGTTGATTTTGTAGTCAACGTAGGTGGACATGTTTTTGTTGAAGTAGTAGGTAGCACCAACATCAACATATTTCAGGATATCTTCGTCGTCGTAGCCACGACCCAGGTTTTTACCTTTAGAC  >  minE/1439264‑1439402

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