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 R2 162 60.6 4616657 98.5% 4547407 62.1

Breseq alignment

BRESEQ :: Evidence
Predicted mutation
evidence seq id position mutation freq annotation gene description
RA W3110S.gb 1,199,872 T→C 10.9% intergenic (‑58/‑400) ymfE ← / → lit predicted inner membrane protein/cell death peptidase, inhibitor of T4 late gene expression

Read alignment evidence...
  seq id position ref new freq score (cons/poly) reads annotation genes product
*W3110S.gb1,199,8720TC10.9% 143.5 / 9.7 55intergenic (‑58/‑400)ymfE/litpredicted inner membrane protein/cell death peptidase, inhibitor of T4 late gene expression
Reads supporting (aligned to +/- strand):  ref base T (25/24);  new base C (3/3);  total (28/27)
Fisher's exact test for biased strand distribution p-value = 1.00e+00
Kolmogorov-Smirnov test that lower quality scores support variant p-value = 9.82e-01

CATATTATTCACCTGAGTCACGCTTTAGGATAGTGTAATGGTAATATTTAATTAAGTGTCATTATATACTTTTCAGTAGGTTAGTTACAATTTTTTGTATCTGTTCAGGCTGACCTAGCTTCGCTGACAGACAATATTG  >  W3110S.gb/1199803‑1199941
                                                                     |                                                                     
cATATTATTCACCTGAGTCACGCTTTAGGATAGTGTAATGGTAATATTTAATTAAGTGTCATTATATACtt                                                                      <  1:1913409/71‑1 (MQ=255)
  tattatTCACCTGAGTCACGCTTTAGGATAGTGTAATGGTAATATTTAATTAAGTGTCATTATATACtttt                                                                    <  1:439801/71‑1 (MQ=255)
  tattatTCACCTGAGTCACGCTTTAGGATAGTGTAATGGTAATATTTAATTAAGTGTCATTATATACtttt                                                                    <  1:508073/71‑1 (MQ=255)
      attCACCTGAGTCACGCTTTAGGATAGTGTAATGGTAATATTTAATTAAGTGTCATTATATACTTTTCAg                                                                 <  1:503171/70‑1 (MQ=255)
       ttCACCTGAGTCACGCTTTAGGATAGTGTAATGGTAATATTTAATTAAGTGTCATTATATACTTTTCAg                                                                 >  1:794876/1‑69 (MQ=255)
             tGAGTCACGCTTTAGGATAGTGTAATGGTAATATTTAATTAAGTGTCATTATATACTTTTCAGTAGgttag                                                         >  1:3570164/1‑71 (MQ=255)
             tGAGTCACGCTTTAGGATAGTGTAATGGTAATATTTAATTAAGTGTCATTATATACCTTTCAGTAGgttag                                                         >  1:849677/1‑71 (MQ=255)
             tGAGTCACGCTTTAGGATAGTGTAATGGTAATATTTAATTAAGTGTCATTATATACCTTTCAGTAGgttag                                                         >  1:3668719/1‑71 (MQ=255)
              gAGTCACGCTTTAGGATAGTGTAATGGTAATATTTAATTAAGTGTCATTATATACTTTTCAGTAGgttagt                                                        >  1:3774903/1‑71 (MQ=255)
              gAGTCACGCTTTAGGATAGTGTAATGGTAATATTTAATTAAGTGTCATTATATACTTTTCAGTAGgttag                                                         >  1:4564791/1‑70 (MQ=255)
               aGTCACGCTTTAGGATAGTGTAATGGTAATATTTAATTAAGTGTCATTATATACTTTTCAGTAGgttag                                                         >  1:316282/1‑69 (MQ=255)
                gTCACGCTTTAGGATAGTGTAATGGTAATATTTAATTAAGTGTCATTATATACTTTTCAGTAGgttagtta                                                      >  1:1451357/1‑71 (MQ=255)
                 tCACGCTTTAGGATAGTGTAATGGTAATATTTAATTAAGTGTCATTATATACTTTTCAGTAGGTTAGTTAc                                                     <  1:1578927/71‑1 (MQ=255)
                   aCGCTTTAGGATAGTGTAATGGTAATATTTAATTAAGTGTCATTATATACTTTTCAGTAGgtt                                                           <  1:250648/63‑1 (MQ=255)
                   aCGCTTTAGGATAGTGTAATGGTAATATTTAATTAAGTGTCATTATATACTTTTCAGTAGGTTAGTTACaa                                                   <  1:458706/71‑1 (MQ=255)
                   aCGCTTTAGGATAGTGTAATGGTAATATTTAATTAAGTGTCATTATATACTTTTCAGTAGGTTAGTTACaa                                                   <  1:2842879/71‑1 (MQ=255)
                    cGCTTTAGGATAGTGTAATGGTAATATTTAATTAAGTGTCATTATATACTTTTCa                                                                  >  1:4443045/1‑55 (MQ=255)
                        ttAGGATAGTGTAATGGTAATATTTAATTAAGTGTCATTATATACTTTTCAGTAGGTTAGTTACAAttttt                                              >  1:827381/1‑71 (MQ=255)
                         tAGGATAGTGTAATGGTAATATTTAATTAAGTGTCATTATATACTTTTCAGTAGGTTAGTTACAAtttttt                                             >  1:1700862/1‑71 (MQ=255)
                           ggATAGTGTAATGGTAATATTTAATTAAGTGTCATTATATACTTTTCAGTAGGTTAGTTACAATTTTTTGt                                           <  1:4300519/71‑1 (MQ=255)
                            gATAGTGTAATGGTAATATTTAATTAAGTGTCATTATATACCTTTCAGTAGGTTAGTTACAATTTTTTGTa                                          >  1:3843456/1‑71 (MQ=255)
                              tAGTGTAATGGTAATATTTAATTAAGTGTCATTATATACTTTTCAGTAGGTTAGTTACAATTTTTTGTATc                                        >  1:3422423/1‑71 (MQ=255)
                                 tgtAATGGTAATATTTAATTAAGTGTCATTATATACTTTTCAGTAGGTTAGTTACAATTTTTTGTATCTGt                                     <  1:3648138/71‑1 (MQ=255)
                                  gtAATGGTAATATTTAATTAAGTGTCATTATATACTTTTCAGTAGGTTAGTTACAAtttt                                               <  1:4339861/60‑1 (MQ=255)
                                   tAATGGTAATATTTAATTAAGTGTCATTATATACTTTTCAGTAGGTTAGTTACAAtt                                                 >  1:1780266/1‑57 (MQ=255)
                                   tAATGGTAATATTTAATTAAGTGTCATTATATACTTTTCAGTAGGTTAGTTACAATTTTTTGTATCTGtt                                    >  1:616161/1‑70 (MQ=255)
                                    aaTGGTAATATTTAATTAAGTGTCATTATATACtt                                                                      <  1:1186514/35‑1 (MQ=255)
                                     aTGGTAATATTTAATTAAGTGTCATTATATACTTTTCAGTAGGTTAGTTACAAttttt                                              <  1:966548/58‑1 (MQ=255)
                                     aTGGTAATATTTAATTAAGTGTCATTATATACTTTTCAGTAGGTTAGTTACAATTTTTTGTATCTGTTCAg                                 <  1:3064455/71‑1 (MQ=255)
                                      tGGTAATATTTAATTAAGTGTCATTATATACTTTTCAGTAGGTTAGTTACAATTTTTTGTATCTGTTCAgg                                >  1:3297484/1‑71 (MQ=255)
                                      tGGTAATATTTAATTAAGTGTCATTATATACTTTTCAGTAGGTTAGTTACAATTTTTTGTATCTGTTCAgg                                >  1:104514/1‑71 (MQ=255)
                                         tAATATTTAATTAAGTGTCATTATATACTTTTCAGTAGGTTAGTTACAATTTTTTGTATCTGTTCAGGCt                              <  1:3409706/70‑1 (MQ=255)
                                         tAATATTTAATTAAGTGTCATTATATACTTTTCAGTAGGTTAGTTACAATTTTTTGTATCTGTTCAGGCt                              >  1:4474772/1‑70 (MQ=255)
                                         tAATATTTAATTAAGTGTCATTATATACCTTTCAGTAGGTTAGTTACAATTTTTTGTATCTGTTCAGGCTg                             <  1:1980860/71‑1 (MQ=255)
                                              tttAATTAAGTGTCATTATATACTTTTCAGTAGGTTAGTTACAATTTTTTGTATCTGTTCAGGCTg                             <  1:772194/66‑1 (MQ=255)
                                              tttAATTAAGTGTCATTATATACTTTTCAGTAGGTTAGTTACAATTTTTTGTATCTGTTCAGGCTGACCTa                        <  1:2976531/71‑1 (MQ=255)
                                                taattaaGTGTCATTATATACTTTTCAGTAGGTTAGTTACAATTTTTTGTATCTGTTCAGGCTGACCTAGc                      >  1:3135950/1‑71 (MQ=255)
                                                  attaaGTGTCATTATATACTTTTCAGTAGGTTAGTTACAATTTTTTGTATCTGTTCAGGCTGACCTAGCt                     <  1:1313590/70‑1 (MQ=255)
                                                  attaaGTGTCATTATATACTTTTCAGTAGGTTAGTTACAATTTTTTGTATCTGTTCAGGCTGACCTAGCt                     <  1:2048223/70‑1 (MQ=255)
                                                   ttaaGTGTCATTATATACTTTTCAGTAGGTTAGTTACAATTTTTTGTATCTGTTCAGGCTGACCTAGCTTc                   <  1:2156196/71‑1 (MQ=255)
                                                      aGTGTCATTATATACTTTTCAGTAGGTTAGTTACAATTTTTTGTATCTGTTCAGGCTGACCTAGCTTCg                  <  1:2593771/69‑1 (MQ=255)
                                                       gtgtCATTATATACTTTTCAGTAGGTTAGTTACAATTTTTTGTATCTGTTCAGGCTGACCTAGCTTCGCTg               <  1:2639384/71‑1 (MQ=255)
                                                        tgtCATTATATACCTTTCAGTAGGTTAGTTACAATTTTTTGTATCTGTTCAGGCTGACCTAGCTTCGCTg               <  1:3535790/70‑1 (MQ=255)
                                                         gtCATTATATACTTTTCAGTAGGTTAGTTACAATTTTTTGt                                           <  1:3697354/41‑1 (MQ=255)
                                                         gtCATTATATACTTTTCAGTAGGTTAGTTACAATTTTTTGTATCTGTTCAgg                                >  1:3426911/1‑52 (MQ=255)
                                                           cATTATATACTTTTCAGTAGGTTAGTTACAATTTTTTGTATCTGTTCAGGCTGACCTAGCTTCGCTga              >  1:1636413/1‑68 (MQ=255)
                                                            aTTATATACTTTTCAGTAGGTTAGTTACAATTTTTTGTATCTGt                                     >  1:3612699/1‑44 (MQ=255)
                                                            aTTATATACTTTTCAGTAGGTTAGTTACAATTTTTTGTATCTGTTCAGGCTg                             >  1:2576641/1‑52 (MQ=255)
                                                            aTTATATACTTTTCAGTAGGTTAGTTACAATTTTTTGTATCTGTTCAGGCTGACCTAGCTTCGCTgacaga          >  1:68572/1‑71 (MQ=255)
                                                             ttATATACCTTTCAGTAGGTTAGTTACAATTTTTTGTATCTGtt                                    <  1:75493/44‑1 (MQ=255)
                                                               atataCTTTTCAGTAGGTTAGTTACAATTTTTTGTATCt                                       >  1:890326/1‑39 (MQ=255)
                                                                tataCTGTTCAGTAGGTTAGTTACAATTTTTTGTATCTGTTCa                                  >  1:600288/1‑43 (MQ=255)
                                                                  taCTTTTCAGTAGGTTAGTTACAATTTTTTGTATCTGt                                     <  1:2327861/38‑1 (MQ=255)
                                                                  taCTTTTCAGTAGGTTAGTTACAATTTTTTGTATCTGTTCAGGCTg                             <  1:2295120/46‑1 (MQ=255)
                                                                   aCTTTTCAGTAGGTTAGTTACAATTTTTTGTATCTGTTCAGGCTGAc                           >  1:127278/1‑47 (MQ=255)
                                                                    cTTTTCAGTAGGTTAGTTACAATTTTTTGTATCTGTTCAGGCTGa                            <  1:2463177/45‑1 (MQ=255)
                                                                    cTTTTCAGTAGGTTAGTTACAATTTTTTGTATCTGTTCAGGCTGa                            <  1:2605436/45‑1 (MQ=255)
                                                                    cTTTTCAGTAGGTTAGTTACAATTTTTTGTATCTGTTCAGGCTGACCTAGCTTCGCTGACAGACAATATtg  >  1:539197/1‑71 (MQ=255)
                                                                    cTTTTCAGTAGGTTAGTTACAATTTTTTGTATCTGTTCAGGCTGACCTAGCTTCGCTGACAGACAATATtg  <  1:2144669/71‑1 (MQ=255)
                                                                     ttttCAGTAGGTTAGTTACAATTTTTTGTATCTGTTCAGGCTGACCTAGCTTCGCTgacaga          >  1:1944985/1‑62 (MQ=255)
                                                                     |                                                                     
CATATTATTCACCTGAGTCACGCTTTAGGATAGTGTAATGGTAATATTTAATTAAGTGTCATTATATACTTTTCAGTAGGTTAGTTACAATTTTTTGTATCTGTTCAGGCTGACCTAGCTTCGCTGACAGACAATATTG  >  W3110S.gb/1199803‑1199941

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