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
A4 F21 I0 R1 1009 73.8 4146436 87.4% 3623985 60.3

Breseq alignment

BRESEQ :: Evidence
Predicted mutation
evidence seq id position mutation freq annotation gene description
RA minE 1,568,107 C→T 19.6% G407R (GGG→AGG)  mntH ← manganese/divalent cation transporter

Read alignment evidence...
  seq id position ref new freq score (cons/poly) reads annotation genes product
*minE1,568,1070CT19.6% 123.0 / 21.3 56G407R (GGG→AGG) mntHmanganese/divalent cation transporter
Reads supporting (aligned to +/- strand):  ref base C (23/22);  new base T (5/6);  total (28/28)
Fisher's exact test for biased strand distribution p-value = 1.00e+00
Kolmogorov-Smirnov test that lower quality scores support variant p-value = 1.00e+00

GCGTTTACGCCGCATCCGCCAATAGTGCCAGATGCGACGCTCATTCAACTACAATCCCAGCGCCGTCCCCACCAACAACCAGATATTCAGCGCCACGACCAGCACCACAATCACCCAGCCTGTCTGTTTTACGCGTTT  >  minE/1568039‑1568176
                                                                    |                                                                     
gCGTTTACGCCGCATCCGCCAATAGTGCCAGATGCGACGCTCATTCAACTACAATCCAAGCGCCGTCCcca                                                                     >  1:3384708/1‑71 (MQ=255)
gCGTTTACGCCGCATCCGCCAATAGTGCCAGATGCGACGCTCATTCAACTACAATCCAAGCGCCGTCCcca                                                                     >  1:3379807/1‑71 (MQ=255)
     tACGCCGCATCCGCCAATAGTGCCAGATGCGACGCTCATTCAACTACAATCCCAGCGCCGTCCTCACcaa                                                                 >  1:712594/1‑70 (MQ=255)
         ccgcATCCGCCAATAGTGCCAGATGCGACGCTCATTCAACTACAATCCCAGCGCCGTCCCCACcaa                                                                 >  1:518673/1‑66 (MQ=255)
          cgcATCCGCCAATAGTGCCAGATGCGACGCTCATTCAACTACAATCCCAGCGCCGTCCTCACCAACAACCa                                                           <  1:2266581/71‑1 (MQ=255)
              tCCGCCAATAGTGCCAGATGCGACGCTCATTCAACTACAATCCCAGCGCCGTCCCCACCAACAACCAGata                                                       >  1:978527/1‑71 (MQ=255)
              tCCGCCAATAGTGCCAGATGCGACGCTCATTCAACTACAATCCCAGCGCCGTCCCCACCAACAACCAGata                                                       <  1:3396016/71‑1 (MQ=255)
                cGCCAATAGTGCCAGATGCGACGCTCATTCAACTACAATCCCAGCGCCGTCCTCACCAACAACCAGATAtt                                                     >  1:1931087/1‑71 (MQ=255)
                cGCCAATAGTGCCAGATGCGACGCTCATTCAACTACAATCCCAGCGCCGTCCCCACCAACAACCAGATAtt                                                     >  1:3152413/1‑71 (MQ=255)
                cGCCAATAGTGCCAGATGCGACGCTCATTCAACTACAATCCCAGCGCCGTCCCCACCAACAACCAGATAtt                                                     >  1:559181/1‑71 (MQ=255)
                cGCCAATAGTGCCAGATGCGACGCTCATTCAACTACAATCCCAGCGCCGTCCCCACCAACAACCAGATAtt                                                     >  1:3823472/1‑71 (MQ=255)
                  ccAATAGTGCCAGATGCGACGCTCATTCAACTACAATCCCAGCGCCGTCCCCACCAACAACCAGATATTc                                                    <  1:818908/70‑1 (MQ=255)
                   cAATAGTGCCAGATGCGACGCTCATTCAACTACAATCCCAGCGCCGTCCCCACCAACAACCAGa                                                         >  1:2882974/1‑64 (MQ=255)
                       aGTGCCAGATGCGACGCTCATTCAACTACAATCCCAGCGCCGTCCCCACCAACAACCAGATATTc                                                    >  1:89894/1‑65 (MQ=255)
                        gTGCCAGATGCGACGCTCATTCAACTACAATCCCAGCGCCGTCCTCACCAACAACCAGATATTCAGCGcc                                              <  1:4007457/70‑1 (MQ=255)
                        gTGCCAGATGCGACGCTCATTCAACTACAATCCCAGCGCCGTCCCAACCAACAACCAGATATTc                                                    >  1:1933937/1‑64 (MQ=255)
                           ccAGATGCGACGCTCATTCAACTACAATCCCAGCGCCGTCCCCACCAACAACCAGATATTCAGCGCCACg                                           <  1:3173580/70‑1 (MQ=255)
                              gATGCGACGCTCATTCAACTACAATCCCAGCGCCGTCCCCACcaac                                                                <  1:1562422/46‑1 (MQ=255)
                              gATGCGACGCTCATTCAACTACAATCCCAGCGCCGTCCCCACCAACAACCAGata                                                       >  1:2004107/1‑55 (MQ=255)
                              gATGCGACGCTCATTCAACTACAATCCCAGCGCCGTCCCCACCAACAACCAGATATTCAGCGCCACGACCa                                       <  1:2765413/71‑1 (MQ=255)
                               aTGCGACGCTCATTCAACTACAATCCCAGCGCCGTCCCCACCAACAACCAGATAtt                                                     <  1:135493/56‑1 (MQ=255)
                               aTGCGACGCTCATTCAACTACAATCCCAGCGCCGTCCCCACCAACAACCAGATATTCAGCGCCACGACCAg                                      <  1:3269817/71‑1 (MQ=255)
                                tGCGACGCTCATTCAACTACAATCCCAGCGCCGTCCTCACCAACAACCAGa                                                         <  1:3762436/51‑1 (MQ=255)
                                tGCGACGCTCATTCAACTACAATCCCAGCGCCGTCCCCACCAACAACCa                                                           <  1:1959068/49‑1 (MQ=255)
                                tGCGACGCTCATTCAACTACAATCCCAGCGCCGTCCCCACCAACAACCAGATATTCAGCGCCACGACCAGc                                     <  1:4066445/71‑1 (MQ=255)
                                tGCGACGCTCATTCAACTACAATCCCAGCGCCGTCCCCACCAACAACCAGATATTCAGCGCCACGACCAGc                                     <  1:101336/71‑1 (MQ=255)
                                 gCGACGCTCATTCAACTACAATCCCAGCGCCGTCCTCACCAACAACCAGata                                                       >  1:2517391/1‑52 (MQ=255)
                                 gCGACGCTCATTCAACTACAATCCCAGCGCCGTCCTCACCAACAACCAGata                                                       >  1:3598780/1‑52 (MQ=255)
                                 gCGACGCTCATTCAACTACAATCCCAGCGCCGTCCCCACCAACAACCa                                                           >  1:229394/1‑48 (MQ=255)
                                 gCGACGCTCATTCAACTACAATCCCAGCGCCGTCCCCACCAACAACCAGATATTCAGCGCCACGACCAGca                                    >  1:407086/1‑71 (MQ=255)
                                    aCGCTCATTCAACTACAATCCCAGCGCCGTCCTCACCAACAACCAGATATTCAGCGCCACg                                           <  1:148860/61‑1 (MQ=255)
                                        tCATTCAACTACAATCCCAGCGCCGTCCCCACCAACAACCAGATATTCAGCGCCACGACCAGcgcca                                 >  1:2516690/1‑67 (MQ=255)
                                        tCATTCAACTACAATCCCAGCGCCGTCCCCACCAACAACCAGATATTCAGCGCCACGACCAGCACCACAAt                             >  1:750857/1‑71 (MQ=255)
                                           ttCAACTACAATCCCAGCGCCGTCCTCACCAACAACCAGATATTCAGCGCCACGACCAGCACCACAATCAc                          <  1:2138776/71‑1 (MQ=255)
                                           ttCAACTACAATCCCAGCGCCGTCCTCACCAACAACCAGATATTCAGCGCCACGACCAGCACCACAATCAc                          <  1:3891811/71‑1 (MQ=255)
                                           ttCAACTACAATCCCAGCGCCGTCCCCACCAACAACCAGATATTCAGCGCCACGACCAGCACCACAATc                            <  1:2334176/69‑1 (MQ=255)
                                           ttCAACTACAATCCCAGCGCCGTCCCCACCAACAACCAGATATTCAGCGCCACGACCAGCACCACAATCAc                          <  1:2858596/71‑1 (MQ=255)
                                           ttCAACTACAATCCCAGCGCCGTCCCCACCAACAACCAGATATTCAGCCCCACGACCAGCACcaca                               <  1:123869/66‑1 (MQ=255)
                                             cAACTACAATCCCAGCGCCGTCCCCACCAACAACCAGATATTCAGCGcccc                                            >  1:1699661/1‑49 (MQ=255)
                                             cAACTACAATCCCAGCGCCGTCCCCACCAACAACAAGATATTCa                                                   >  1:923421/1‑44 (MQ=255)
                                              aaCTACAATCCCAGCGCCGTCCCCACCAACAACCAGATATTCAGCGCCACGACCAGCACCACAATCAcc                         >  1:2725090/1‑69 (MQ=255)
                                                cTACAATCCCAGCGCCGTCCCCACCAACAACCAGATATTCAGCGCCACGACCAGCACcaca                               <  1:396063/61‑1 (MQ=255)
                                                cTACAATCCCAGCGCCGTCCCCACCAACAACCAGATATTCAGCGCCACGACCAGCACCACAATCACCCAGc                     <  1:3467598/71‑1 (MQ=255)
                                                cTACAATCCCAGCGCCGTCCCCACCAACAACCAGATATTCAGCGCCACGACCAGCACCACAATCACCCAGc                     <  1:2593883/71‑1 (MQ=255)
                                                  aCAATCCCAGCGCCGTCCCCACCAACAACCAGATATTCAGCGCCACGACCa                                       >  1:2360164/1‑51 (MQ=255)
                                                  aCAATCCCAGCGCCGTCCCCACCAACAACCAGATATTCAGCGCCACGACCAGCACCACAATCACCCAGCct                   >  1:1989092/1‑71 (MQ=255)
                                                  aCAATCCCAGCGCCGTCCCCACCAACAACCAGATATTCAGCGCCACGACCAGCACCACAATCACCCAGCct                   >  1:141683/1‑71 (MQ=255)
                                                   cAATCCCAGCGCCGTCCTCACCAACAACCAGATATTCAGCGCCACGACCAGCACCACAATCAc                          >  1:3664521/1‑63 (MQ=255)
                                                    aaTCCCAGCGCCGTCCCCACCAACAACCAGATATTCAGCGCCACGACCAGCACCACAATCACCCAGCctgt                 >  1:3449315/1‑71 (MQ=255)
                                                       cccAGCGCCGTCCCCACCAACAACCAGATATTCAGCGCCAc                                            >  1:3292954/1‑41 (MQ=255)
                                                        ccAGCGCCGTCCCCACCAACAACCAGATATTCAGCGCCACGACCAGCACCACAATCACCCAGCctgtctgt             <  1:770085/71‑1 (MQ=255)
                                                          aGCGCCGTCCCCACCAACAACCAGATATTCAGCGCCACGACCAGCACCACAATCACCCAGCCTGTCTGttt           <  1:574478/71‑1 (MQ=255)
                                                          aGCGCCGTCCCCACCAACAACCAGATATTCAGCGCCACGACCAGCACCACAATCACCCAGCCTGTCTGttt           <  1:825005/71‑1 (MQ=255)
                                                          aGCGCCGTCCCCACCAACAACCAGATATTCAGCGCCACGACCAGCACCACAATCACCCAGCCTGTCTGttt           <  1:3299601/71‑1 (MQ=255)
                                                           gcgcCGTCCCCACCAACAACCAGATATTCAGCGCCACGACCAGcaccac                                <  1:1281996/49‑1 (MQ=255)
                                                              ccGTCCCCACCAACAACCAGATATTCAGCGCCACGACCAGCACCACAAt                             <  1:2826491/49‑1 (MQ=255)
                                                               cGTCCCCACCAACAACCAGATATTCAGCGCCACGACCAGCACCACAATCACCCAGCCTGTCTGTTTTAcgc      >  1:4077066/1‑71 (MQ=255)
                                                                gTCCCCACCAACAACCAGATATTCAGCGCCACGACCAGCACCACAATCACCCAGcc                    >  1:1737592/1‑56 (MQ=255)
                                                                   cccACCAACAACCAGATATTCAGCGCCACGACCAGCACCACAATCACCCAGCCTGTCTGTTTTACGCGttt  >  1:2527841/1‑71 (MQ=255)
                                                                   cccACCAACAACCAGATATTCAGCGCCACGACCAGCACCACAATCACCCAGCCTGTCTGTTTTACGCGttt  >  1:2522862/1‑71 (MQ=255)
                                                                   cccACCAACAACCAGATATTCAGCGCCACGACCAGCACCACAATCACCCAGCCTGTCTGTTTTACGCGtt   >  1:1534141/1‑70 (MQ=255)
                                                                    |                                                                     
GCGTTTACGCCGCATCCGCCAATAGTGCCAGATGCGACGCTCATTCAACTACAATCCCAGCGCCGTCCCCACCAACAACCAGATATTCAGCGCCACGACCAGCACCACAATCACCCAGCCTGTCTGTTTTACGCGTTT  >  minE/1568039‑1568176

Alignment Legend
Aligned base mismatch/match (shaded by quality score): ATCG/ATCG < 3 ≤ ATCG/ATCG < 14 ≤ ATCG/ATCG < 32 ≤ ATCG/ATCG < 36 ≤ ATCG/ATCG
Unaligned base: atcg    Masked matching base: atcg    Alignment gap: ‑    Deleted base: ‑

GATK/CNVnator alignment

N/A