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
A12 F56 I1 R1 165 53.8 2611523 96.4% 2517508 99.9

Breseq alignment

BRESEQ :: Evidence
Predicted mutation
evidence seq id position mutation annotation gene description
RA NC_000913 2,782,076 T→C V217V (GTA→GTG)  ypjA ← adhesin‑like autotransporter

Read alignment evidence...
  seq id position ref new freq score (cons/poly) reads annotation genes product
*NC_0009132,782,0760TC98.3% 200.1 / ‑4.4 58V217V (GTA→GTG) ypjAadhesin‑like autotransporter
Reads supporting (aligned to +/- strand):  ref base T (1/0);  new base C (32/25);  total (33/25)
Fisher's exact test for biased strand distribution p-value = 1.00e+00
Kolmogorov-Smirnov test that lower quality scores support variant p-value = 9.71e-01

CCACCAGAATAGATATGCGTATTTTTTGCCGTTGACTTACTATTCAGAGACTGAGTTCCGCCTTCAATCGTCGTGTCCAGCGCACGGCTCTCATATACTCTTTGCTCACCGCCATTTTTAATGGTTGTTGTTTCTACTGTGCTCTGTTCAACATACTGTCGACCACCATTTATGGTTGTGTTCGTTGCCAG  >  NC_000913/2781981‑2782171
                                                                                               |                                                                                               
ccaccaGAATAGATATGCGTATTTTTTGCCGTTGACTTACTATTCAGAGACTGAGTTCCGCCTTCAATCGTCGTGTCCAGCGCACGGCTCTCATACActc                                                                                             >  1:351102/1‑100 (MQ=255)
 caccaGAATAGATATGCGTATTTTTTGCCGTTGACTTACTATTCAGAGACTGAGTTCCGCCTTCAATCGTCGTGTCCAGCGCACGGCTCTCATACActct                                                                                            >  2:979557/1‑100 (MQ=255)
 caccaGAATAGATATGCGTATTTTTTGCCGTTGACTTACTATTCAGAGACTGAGTTCCGCCTTCAATCGTCGTGTCCAGCGCACGGCTCTCATACActct                                                                                            <  1:659518/100‑1 (MQ=255)
   ccaGAATAGATATGCGTATTTTTTTTTTTTTTTTTACTATTAAGAGACTGAGTTCCTCCTTCAATTGTCGTGTCCAGCGCACGGCTCTCATACACTCttt                                                                                          >  2:520212/1‑100 (MQ=255)
       aaTAGATATGCGTATTTTTTGCCGTTGACTTACTATTCAGAGACTGAGTTCCGCCTTCAATCGTCGTGTCCAGCGCACGGCTCTCATACACTCTTTGCTc                                                                                      >  2:1006891/1‑100 (MQ=255)
        aTAGATATGCGTATTTTTTGCCGTTGACTTACTATTCAGAGACTGAGTTCCGCCTTCAATCGTCGTGTCCAGCGCACGGCTCTCATACACTCTTTGCTCa                                                                                     <  2:609164/100‑1 (MQ=255)
           gATATGCGTATTTTTTGCCGTTGACTTACTATTCAGAGACTGAGTTCCGCCTTCAATCGTCGTGTCCAGCGCACGGCTCTCATACACTCTTTGCTCACCg                                                                                  >  2:986749/1‑100 (MQ=255)
           gATATGCGTATTTTTTGCCGTTGACTTACTATTCAGAGACTGAGTTCCGCCTTCAATCGTCGTGTCCAGCGCACGGCTCTCATACACTCTTTGCTCACCg                                                                                  <  2:1288942/100‑1 (MQ=255)
             tatGCGTATTTTTTGCCGTTGACTTACTATTCAGAGACTGAGTTCCGCCTTCAATCGTCGTGTCCAGCGCACGGCTCTCATACACTCTTTGCTCACCGcc                                                                                >  1:1027134/1‑100 (MQ=255)
                 cGTATTTTTTGCCGTTGACTTACTATTCAGAGACTGAGTTCCGCCTTCAATCGTCGTGTCCAGCGCGCGGCTCTCATACACTCTTTGCTCCCCGCCAttt                                                                            >  1:707506/1‑100 (MQ=255)
                  gTATTTTTTGCCGTTGACTTACTATTCAGAGACTGAGTTCCGCCTTCAATCGTCGTGTCCAGCGCACGGCTCTCATACACTCTTTGCTCACCGCCAtttt                                                                           >  2:483993/1‑100 (MQ=255)
                   tATTTTTTGCCGTTGACTTACTATTCAGAGACTGAGTTCCGCCTTCAATCGTCGTGTCCAGCGCACGGCTCTCATACACTCTTTGCTCACCGCCAttttt                                                                          >  2:358955/1‑100 (MQ=255)
                    aTTTTTTGCCGTTGACTTACTATTCAGAGACTGAGTTCCGCCTTCAATCGTCGTGTCCAGCGCACGGCTCTCATACACTCTTTGCTCACCGCCATTTTTa                                                                         >  1:237423/1‑100 (MQ=255)
                          tGCCGTTGACTTACTATTCAGAGACTGAGTTCCGCCTTCAATCGTCGTGTCCAGCGCACGGCTCTCATACACTCTTTGCTCACCGCCATTTTTAATGgtt                                                                   >  1:1048056/1‑100 (MQ=255)
                          tGCCGTTGACTTACTATTCAGAGACTGAGTTCCGCCTTCAATCGTCGTGTCCAGCGCACGGCTCTCATACACTCTTTGCTCACCGCCATTTTTAATGgtt                                                                   >  1:1048999/1‑100 (MQ=255)
                           gCCGTTGACTTACTATTCAGAGACTGAGTTCCGCCTTCAATCGTCGTGTCCAGCGCACGGCTCTCATACACTCTTTGCTCACCGCCATTTTTAATGgttg                                                                  <  2:824457/100‑1 (MQ=255)
                            ccGTTGACTTACTATTCAGAGACTGAGTTCCGCCTTCAATCGTCGTGTCCAGCGCACGGCTCTCATACACTCTTTGCTCACCGCCATTTTTAATGgttgt                                                                 <  2:199725/100‑1 (MQ=255)
                            ccGTTGACTTACTATTCAGAGACTGAGTTCCGCCTTCAATCGTCGTGTCCAGCGCACGGCTCTCATACACTCTTTGCTCACCGCCATTTTTAATGgttgt                                                                 >  2:1097831/1‑100 (MQ=255)
                              gTTGACTTACTATTCAGAGACTGAGTTCCGCCTTCAATCGTCGTGTCCAGCGCACGGCTCTCATACACTCTTTGCTCACCGCCATTTTTAATGgttgttg                                                               >  2:289314/1‑100 (MQ=255)
                              gTTGACTTACTATTCAGAGACTGAGTTCCGCCTTCAATCGTCGTGTCCAGCGCACGGCTCTCATACACTCTTTGCTCACCGCCATTTTTAATGgttgttg                                                               >  1:739828/1‑100 (MQ=255)
                                tGACTTACTATTCAGAGACTGAGTTCCGCCTTCAATCGTCGTGTCCAGCGCACGGCTCTCATACACTCTTTGCTCACCGCCATTTTTAATGgttgttgtt                                                             >  2:496406/1‑100 (MQ=255)
                                 gACTTACTATTCAGAGACTGAGTTCCGCCTTCAATCGTCGTGTCCAGCGCACGGCTCTCATACACTCTTTGCTCACCGCCATTTTTAATGGTTGTTGttt                                                            <  2:243394/100‑1 (MQ=255)
                                   cTTACTATTCAGAGACTGAGTTCCGCCTTCAATCGTCGTGTCCAGCGCACGGCTCTCATACACTCTTTGCTCACCGCCATTTTTAATGGTTGTTGTTTCt                                                          <  1:979565/100‑1 (MQ=255)
                                   cTTACTATTCAGAGACTGAGTTCCGCCTTCAATCGTCGTGTCCAGCGCACGGCTCTCATACACTCTTTGCTCACCGCCATTTTTAATGGTTGTTGTTTCt                                                          <  1:749485/100‑1 (MQ=255)
                                     tACTATTCAGAGACTGAGTTCCGCCTTCAATCGTCGTGTCCAGCGCACGGCTCTCATACACTCTTTGCTCACCGCCATTTTTAATGGTTGTTGTTTCTAc                                                        >  2:538432/1‑100 (MQ=255)
                                     tACTATTCAGAGACTGAGTTCCGCCTTCAATCGTCGTGTCCAGCGCACGGCTCTCATACACTCTTTGCTCACCGCCATTTTTAATGGTTGTTGTTTCTAc                                                        <  1:220222/100‑1 (MQ=255)
                                        tATTCAGAGACTGAGTTCCGCCTTCAATCGTCGTGTCCAGCGCACGGCTCTCATACACTCTTTGCTCACCGCCATTTTTAATGGTTGTTGTTTCTACtgt                                                     >  2:889583/1‑100 (MQ=255)
                                           tCAGAGACTGAGTTCCGCCTTCAATCGTCGTGTCCAGCGCACGGCTCTCATACACTCTTTGCTCACCGCCATTTTTAATGGTTGTTGTTTCTACTGTGct                                                  <  1:551315/100‑1 (MQ=255)
                                           tCAGAGACTGAGTTCCGCCTTCAATCGTCGTGTCCAGCGCACGGCTCTCATACACTCTTTGCTCACCGCCATTTTTAATGGTTGTTGTTTCTACTGTGct                                                  >  1:182769/1‑100 (MQ=255)
                                            cAGGGACTGAGTTCCGCCTTCAATCGTCGTGTCCAGCGCACGGCTCTCATACACTCTTTGCTCACCGCCATTTTTAATGGTTGTTGTTTCTACTGTGctc                                                 <  2:1171654/100‑1 (MQ=255)
                                            cAGAGACTGAGTTCCGCCTTCAATCGTCGTGTCCAGCGCACGGCTCTCATACACTCTTTGCTCACCGCCATTTTTAATGGTTGTTGTTTCTACTGTGctc                                                 >  1:567740/1‑100 (MQ=255)
                                                gaCTGAGTTCCGCCTTCAATCGTCGTGTCCAGCGCACGGCTCTCATACACTCTTTGCTCACCGCCATTTTTAATGGTTGTTGTTTCTACTGTGCTCTGtt                                             >  2:630606/1‑100 (MQ=255)
                                                  cTGAGTTCCGCCTTCAATCGTCGTGTCCAGCGCACGGCTCTCATACACTCTTTGCTCACCGCCATTTTTAATGGTTGTTGTTTCTACTGTGCTCTGTTc                                            <  2:478553/99‑1 (MQ=255)
                                                  cTGAGTTCCGCCTTCAATCGTCGTGTCCAGCGCACGGCTCTCATACACTCTTTGCTCACCGCCATTTTTAATGGTTGTTGTTTCTACTGTGCTCTGTTCa                                           >  1:468/1‑100 (MQ=255)
                                                   tGAGTTCCGCCTTCAATCGTCGTGTCCAGCGCACGGCTCTCATACACTCTTTGCTCACCGCCATTTTTAATGGTTGTTGTTTCTACTGTGCTCTGTTCaa                                          >  1:506229/1‑100 (MQ=255)
                                                    gAGTTCCGCCTTCAATCGTCGTGTCCAGCGCACGGCTCTCATACACTCTTTGCTCACCGCCATTTTTAATGGTTGTTGTTTCTACTGTGCTCTGTTCAAc                                         <  1:1109788/100‑1 (MQ=255)
                                                     aGTTCCGCCTTCAATCGTCGTGTCCAGCGCACGGCTCTCATACACTCTTTGCTCACCGCCATTTTTAATGGTTGTTGTTTCTACTGTGCTCTGTTCAACa                                        <  1:128403/100‑1 (MQ=255)
                                                     aGTTCCGCCTTCAATCGTCGTGTCCAGCGCACGGCTCTCATACACTCTTTGCTCACCGCCATTTTTAATGGTTGTTGTTTCTACTGTGCTCTGTTCAACa                                        >  1:1079505/1‑100 (MQ=255)
                                                     aGTTCCGCCTTCAATCGTCGTGTCCAGCGCACGGCTCTCATACACTCTTTGCTCACCGCCATTTTTAATGGTTGTTGTTTCTACTGTGCTCTGTTCAACa                                        <  1:872837/100‑1 (MQ=255)
                                                        tCCGCCTTCAATCGTCGTGTCCAGCGCACGGCTCTCATACACTCTTTGCTCACCGCCATTTTTAATGGTTGTTGTTTCTACTGTGCTCTGTTCAACATAc                                     <  2:1048989/100‑1 (MQ=255)
                                                        tCCGCCTTCAATCGTCGTGTCCAGCGCACGGCTCTCATACACTCTTTGCTCACCGCCATTTTTAATGGTTGTTGTTTCTACTGTGCTCTGTTCAACATAc                                     <  2:1048046/100‑1 (MQ=255)
                                                           gCCTTCAATCGTCGTGTCCAGCGCACGGCTCTCATACACTCTTTGCTCACCGCCATTTTTAATGGTTGTTGTTTCTACTGTGCTCTGTTCAACATACTGt                                  >  1:607154/1‑100 (MQ=255)
                                                           gCCTTCAATCGTCGTGTCCAGCGCACGGCTCTCATACACTCTTTGCTCACCGCCATTTTTAATGGTTGTTGTTTCTACTGTGCTCTGTTCAACATACTGt                                  <  1:538436/100‑1 (MQ=255)
                                                               tCAATCGTCGTGTCCAGCGCACGGCTCTCATACACTCTTTGCTCACCGCCATTTTTAATGGTTGTTGTTTCTACTGTGCTCTGTTCAACATACTGTCGac                              <  1:528703/100‑1 (MQ=255)
                                                                 aaTCGTCGTGTCCAGCGCACGGCTCTCATACACTCTTTGCTCACCGCCATTTTTAATGGTTGTTGTTTCTACTGTGCTCTGTTCAACATACTGTCGacca                            >  1:1046642/1‑100 (MQ=255)
                                                                    cgtcgtGTCCAGCGCACGGCTCTCATACACTCTTTGCTCACCGCCATTTTTAATGGTTGTTGTTTCTACTGTGCTCTGTTCAACATACTGTCGAccacca                         >  2:821332/1‑100 (MQ=255)
                                                                      tcgtGTCCAGCGCACGGCTCTCATACACTCTTTGCTCACCGCCATTTTTAATGGTTGTTGTTTCTACTGTGCTCTGTTCAACATACTGTCGACCACCAtt                       >  1:102101/1‑100 (MQ=255)
                                                                          gtCCAGCGCACGGCTCTCATACACTCTTTGCTCACCGCCATTTTTAATGGTTGTTGTTTCTACTGTGCTCTGTTCAACATACTGTCGACCACCATTTATg                   <  2:402831/100‑1 (MQ=255)
                                                                           tCCAGCGCACGGCTCTCATACACTCTTTGCTCACCGCCATTTTTAATGGTTGTTGTTTCTACTGTGCTCTGTTCAACATACTGTCGACCACCATTTATgg                  <  2:1079495/100‑1 (MQ=255)
                                                                             cAGCGCACGGCTCTCATACACTCTTTGCTCACCGCCATTTTTAATGGTTGTTGTTTCTACTGTGCTCTGTTCAACATACTGTCGACCACCATTTATGGtt                >  2:481660/1‑100 (MQ=255)
                                                                              aGCGCACGGCTCTCATACACTCTTTGCTCACCGCCATTTTTAATGGTTGTTGTTTCTACTGTGCTCTGTTCAACATACTGTCGACCACCATTTATGGTtg               <  2:571893/100‑1 (MQ=255)
                                                                                    cGGCTCTCATACACTCTTTGCTCACCGCCATTTTTAATGGTTGTTGTTTCTACTGTGCTCTGTTCAACATACTGTCGACCACCATTTATGGTTGTGTTCg         >  2:648227/1‑100 (MQ=255)
                                                                                       ctctCATACACTCTTTGCTCACCGCCATTTTTAATGGTTGTTGTTTCTACTGTGCTCTGTTCAACATACTGTCGACCACCATTTATGGTTGTGTTCGTTg      <  1:499546/100‑1 (MQ=255)
                                                                                           cATATACTCTTTGCTCACCGCCATTTTTAATGGTTGTTGTTTCTACTGTGCTCTGTTCAACACACTGTCGACCACCATTTATGGTTGTGTTCGTTGCCAg  >  1:143796/1‑100 (MQ=255)
                                                                                           cATACACTCTTTGCTCACCGCCATTTTTAATGGTTGTTGTTTCTACTGTGCTCTGTTCAACATACTGTCGACCACCATTTATGGTTGTGTTCGTTGCCAg  <  1:1244808/100‑1 (MQ=255)
                                                                                           cATACACTCTTTGCTCACCGCCATTTTTAATGGTTGTTGTTTCTACTGTGCTCTGTTCAACATACTGTCGACCACCATTTATGGTTGTGTTCGTTGCCAg  >  2:827570/1‑100 (MQ=255)
                                                                                           cATACACTCTTTGCTCACCGCCATTTTTAATGGTTGTTGTTTCTACTGTGCTCTGTTCAACATACTGTCGACCACCATTTATGGTTGTGTTCGTTGCCAg  >  1:1278882/1‑100 (MQ=255)
                                                                                           cATACACTCTTTGCTCACCGCCATTTTTAATGGTTGTTGTTTCTACTGTGCTCTGTTCAACATACTGTCGACCACCATTTATGGTTGTGTTCGTTGCCAg  <  1:304226/100‑1 (MQ=255)
                                                                                               |                                                                                               
CCACCAGAATAGATATGCGTATTTTTTGCCGTTGACTTACTATTCAGAGACTGAGTTCCGCCTTCAATCGTCGTGTCCAGCGCACGGCTCTCATATACTCTTTGCTCACCGCCATTTTTAATGGTTGTTGTTTCTACTGTGCTCTGTTCAACATACTGTCGACCACCATTTATGGTTGTGTTCGTTGCCAG  >  NC_000913/2781981‑2782171

Alignment Legend
Aligned base mismatch/match (shaded by quality score): ATCG/ATCG < 3 ≤ ATCG/ATCG < 22 ≤ ATCG/ATCG < 32 ≤ ATCG/ATCG < 41 ≤ ATCG/ATCG
Unaligned base: atcg    Masked matching base: atcg    Alignment gap: ‑    Deleted base: ‑

GATK/CNVnator alignment

N/A