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 F21 I0 R2 316 65.6 5147759 97.4% 5013917 60.3

Breseq alignment

BRESEQ :: Evidence
Predicted mutation
evidence seq id position mutation freq annotation gene description
RA W3110S.gb 702,273 C→T 27.5% D301N (GAT→AAT)  nagA ← N‑acetylglucosamine‑6‑phosphate deacetylase

Read alignment evidence...
  seq id position ref new freq score (cons/poly) reads annotation genes product
*W3110S.gb702,2730CT27.5% 156.0 / 67.0 91D301N (GAT→AAT) nagAN‑acetylglucosamine‑6‑phosphate deacetylase
Reads supporting (aligned to +/- strand):  ref base C (33/33);  new base T (12/13);  total (45/46)
Fisher's exact test for biased strand distribution p-value = 1.00e+00
Kolmogorov-Smirnov test that lower quality scores support variant p-value = 9.67e-01

CAATGTTCGACCAGATTACGCACGCCTTCAATCATGGTTAAGGATGAACCGCTTAACGTACCGTTCTCATCCACACAAAGTCCGTTACGGTAGTATATTGTTTTACCCGCAAAAATGAACTGTTCAATGTTGGCAC  >  W3110S.gb/702203‑702338
                                                                      |                                                                 
cAATGTTCGACCAGATTACGCACGCCTTCAATCATGGTTAAGGATGAACCGCTTAACGTACCGTTCTCATc                                                                   >  1:467061/1‑71 (MQ=255)
cAATGTTCGACCAGATTACGCACGCCTTCAATCATGGTTAAGGATGAACCGCTTAACGTACCGTTCTCATc                                                                   >  1:3164186/1‑71 (MQ=255)
  aTGTTCGACCAGATTACGCACGCCTTCAATCATGGTTAAGGATGAACCGCTTAACGTACCGTTCTCATTca                                                                 <  1:2451385/71‑1 (MQ=255)
   tGTTCGACCAGATTACGCACGCCTTCAATCATGGTTAAGGATGAACCGCTTAACGTACCGTTCTCATCcac                                                                <  1:4517241/71‑1 (MQ=255)
     ttCGACCAGATTACGCACGCCTTCAATCATGGTTAAGGATGAACCGCTTAACGTACCGTTCTCATTcaca                                                               >  1:1451919/1‑70 (MQ=255)
           cAGATTACGCACGCCTTCAATCATGGTTAAGGATGAACCGCTTAACGTACCGTTCTCATTca                                                                 >  1:263219/1‑62 (MQ=255)
           cAGATTACGCACGCCTTCAATCATGGTTAAGGATGAACCGCTTAACGTACCGTTCTCATTca                                                                 >  1:2624606/1‑62 (MQ=255)
           cAGATTACGCACGCCTTCAATCATGGTTAAGGATGAACCGCTTAACGTACCGTTCTCATCCACACAAAGTc                                                        <  1:3042490/71‑1 (MQ=255)
            aGATTACGCACGCCTTCAATCATGGTTAAGGATGAACCGCTTAACGTACCGTTCTCATCCACACAAAGTcc                                                       <  1:1178013/71‑1 (MQ=255)
                 acgcacgcCTTCAATCATGGTTAAGGATGAACCGCTTAACGTACCGTTCTCATCCACACAAAGTCCGt                                                     >  1:2888293/1‑68 (MQ=255)
                 acgcacgcCTTCAATCATGGTTAAGGATGAACCGCTTAACGTACCGTTCTCATCCACACAAAGTCCGt                                                     >  1:2261708/1‑68 (MQ=255)
                 acgcacgcCTTCAATCATGGTTAAGGATGAACCGCTTAACGTACCGTTCTCATCCACACAAAGTCCGt                                                     >  1:5046763/1‑68 (MQ=255)
                 acgcacgcCTTCAATCATGGTTAAGGATGAACCGCTTAACGTACCGTTCTCATCCACACAAAGTCCGt                                                     >  1:78012/1‑68 (MQ=255)
                  cgcacgcCTTCAATCATGGTTAAGGATGAACCGCTTAACGTACCGTTCTCATCCACACAAAGTCCGTTAc                                                  <  1:3282097/70‑1 (MQ=255)
                    cacgcCTTCAATCATGGTTAAGGATGAACCGCTTAACGTACCGTTCTCATCCACACAAAGTCCGTTACgg                                                >  1:4293696/1‑70 (MQ=255)
                    cacgcCATCAATCATGGTTAAGGATGAACCGCTTAACGTACCGTTCTCATCCACACAAAGTCCGTTACgg                                                >  1:1190/1‑70 (MQ=255)
                        ccTTCAATCATGGTTAAGGATGAACCGCTTAACGTACCGTTCTCATCCACACAAAGTCCGTTACGgtagta                                           <  1:1853072/71‑1 (MQ=255)
                          ttCAATCATGGTTAAGGATGAACCGCTTAACGTACCGTTCTCATTcacac                                                              <  1:3838360/50‑1 (MQ=255)
                           tCAATCATGGTTAAGGATGAACCGCTTAACGTACCGTTCTCATCCACACAAAGTc                                                        >  1:2735227/1‑55 (MQ=255)
                           tCAATCATGGTTAAGGATGAACCGCTTAACGTACCGTTCTCATCCACACAAAGTCCGt                                                     <  1:1030050/58‑1 (MQ=255)
                           tCAATCATGGTTAAGGATGAACCGCTTAACGTACCGTTCTCATCCACACAAAGTCCGt                                                     <  1:832659/58‑1 (MQ=255)
                           tCAATCATGGTTAAGGATGAACCGCTTAACGTACCGTTCTCATCCACACAAAGTCCGt                                                     <  1:679024/58‑1 (MQ=255)
                           tCAATCATGGTTAAGGATGAACCGCTTAACGTACCGTTCTCATCCACACAAAGTCCGt                                                     <  1:4678436/58‑1 (MQ=255)
                            cAATCATGGTTAAGGATGAACCGCTTAACGTACCGTTCTCATTCACACAAAGTCCGTTACGGTAGTatat                                        >  1:2266335/1‑70 (MQ=255)
                            cAATCATGGTTAAGGATGAACCGCTTAACGTACCGTTCTCATCCACACAAAGTCCGTTACGGTAGTATAtt                                       >  1:2055841/1‑71 (MQ=255)
                            cAATCATGGTTAAGGATGAACCGCTTAACGTACCGTTCTCATCCACACAAAGTCCGTTACGGTAGTATAtt                                       >  1:4567691/1‑71 (MQ=255)
                              aTCATGGTTAAGGATGAACCGCTTAACGTACCGTTCTCATCCACACAAAGTCCGTTACGgtagta                                           <  1:5144204/65‑1 (MQ=255)
                              aTCATGGTTAAGGATGAACCGCTTAACGTACCGTTCTCATCCACACAAAGTCCGTTACGgtagta                                           <  1:2072529/65‑1 (MQ=255)
                              aTCATGGTTAAGGATGAACCGCTTAACGTACCGTTCTCATCCACACAAAGTCCGTTACGGTAGTATATTGt                                     <  1:2143377/71‑1 (MQ=255)
                              aTCATGGTTAAGGATGAACCGCTTAACGTACCGTTCTCATCCACACAAAGTCCGTTACGGTAGTATATTGt                                     <  1:512002/71‑1 (MQ=255)
                               tCATGGTTAAGGATGAACCGCTTAACGTACCGTTCTCATCCACACAAAGTCCGTTACGGTAGTATATTGtt                                    >  1:1976993/1‑71 (MQ=255)
                                cATGGTTAAGGATGAACCGCTTAACGTACCGTTCTCATCCACACAAAGTCCGTTa                                                   >  1:4661397/1‑55 (MQ=255)
                                cATGGTTAAGGATGAACCGCTTAACGTACCGTTCTCATCCACACAAAGTCCGTTa                                                   >  1:4330493/1‑55 (MQ=255)
                                cATGGTTAAGGATGAACCGCTTAACGTACCGTTCTCATCCACACAAAGTCCGTTa                                                   >  1:4410175/1‑55 (MQ=255)
                                cATGGTTAAGGATGAACCGCTTAACGTACCGTTCTCATCCACACAAAGTCCGTTa                                                   >  1:2730550/1‑55 (MQ=255)
                                cATGGTTAAGGATGAACCGCTTAACGTACCGTTCTCATCCACACAAAGTCCGTTa                                                   >  1:3248906/1‑55 (MQ=255)
                                 aTGGTTAAGGATGAACCGCTTAACGTACCGTTCTCATTCACACAAAGTCCGTTACGGTAGTATATTGtttt                                  <  1:915027/71‑1 (MQ=255)
                                 aTGGTTAAGGATGAACCGCTTAACGTACCGTTCTCATTCACACAAAGTCCGTTACGGTAGTATATTGtttt                                  <  1:3702922/71‑1 (MQ=255)
                                 aTGGTTAAGGATGAACCGCTTAACGTACCGTTCTCATTCACACAAAGTCCGTTACGGTAGTATATTGttt                                   >  1:1740340/1‑70 (MQ=255)
                                 aTGGTTAAGGATGAACCGCTTAACGTACCGTTCTCATCca                                                                 >  1:1158688/1‑40 (MQ=255)
                                 aTGGTTAAGGATGAACCGCTTAACGTACCGTTCTCATCCACACAAAGTCCGTTACGGTAGTATATTGttt                                   >  1:971060/1‑70 (MQ=255)
                                 aTGGTTAAGGATGAACCGCTTAACGTAACGTTCTCATTCACACAAAGTCCGTTACGGTAGTATATTGtttt                                  <  1:4314427/71‑1 (MQ=255)
                                  tGGTTAAGGATGAACCGCTTAACGTACCGTTCTCATTCACACAAAGTCCGTTACGGTAGTATATTGtttt                                  <  1:3721317/70‑1 (MQ=255)
                                   ggTTAAGGATGAACCGCTTAACGTACCGTTCTCATCCACACAAAg                                                          >  1:5062563/1‑45 (MQ=255)
                                    gTTAAGGATGAACCGCTTAACGTACCGTTCTCATCCACACAAAGTCCGTTACGGTAGTATATTGTTTTAc                                <  1:1962607/70‑1 (MQ=255)
                                     ttAAGGATGAACCGCTTAACGTACCGTTCTCATTCACACAAAGTCCGTTACGGTAGTATATTGtttt                                  <  1:1320413/67‑1 (MQ=255)
                                     ttAAGGATGAACCGCTTAACGTACCGTTCTCATTCACACAAAGTCCGTTACGGTAGTATATTGtttt                                  <  1:650559/67‑1 (MQ=255)
                                     ttAAGGATGAACCGCTTAACGTACCGTTCTCATCcacaca                                                             <  1:3030434/40‑1 (MQ=255)
                                     ttAAGGATGAACCGCTTAACGTACCGTTCTCATCcacaca                                                             <  1:4299235/40‑1 (MQ=255)
                                        aGGATGAACCGCTTAACGTACCGTTCTCATCCACACAAAGt                                                         >  1:1771144/1‑41 (MQ=255)
                                           aTGAACCGCTTAACGTACCGTTCTGATCCACACAAAGTCCGTTACGGTAGTATATTGTTTTACCCGCaaa                         >  1:2139746/1‑70 (MQ=255)
                                           aTGAACCGCTTAACGTACCGTTCTCATCCACACAAAGTCCGTTACGgta                                              >  1:5061166/1‑49 (MQ=255)
                                           aTGAACCGCTTAACGTACCGTTCTCATCCACACAAAGTCCGTTACGGTAGTATATTGTTTTACCCGCaaa                         >  1:3280939/1‑70 (MQ=255)
                                            tGAACCGCTTAACGTACCGTTCTCATCCACACAAAGTCCGt                                                     <  1:4734470/41‑1 (MQ=255)
                                             gAACCGCTTAACGTACCGTTCTCATTCACACAAAGTCCGTTACGGTAGTATATTGTTTTACCCGCAAAAAt                      >  1:4826338/1‑71 (MQ=255)
                                             gAACCGCTTAACGTACCGTTCTCATCCACACAAAGTCCGTTACGgtagta                                           >  1:29018/1‑50 (MQ=255)
                                             gAACCGCTTAACGTACCGTTCTCATCCACACAAAGTCCGTTACGGTAGTATATTGTTTTACCCGCAAAAAt                      >  1:4762020/1‑71 (MQ=255)
                                             gAACCGCTTAACGTACCGTTCTCATCCACACAAAGTCCGTTACGGTAGTATATTGTTTTACCCGCAAAAAt                      >  1:4756012/1‑71 (MQ=255)
                                              aaCCGCTTAACGTACCGTTCTCATTCACACAAAGTCCGTTACGGTAGTATATTGTTTTACCCGCAAAAAt                      >  1:2112833/1‑70 (MQ=255)
                                              aaCCGCTTAACGTACCGTTCTCATTCACACAAAGTCCGTTACGGTAGTATATTGTTTTACCCGCAAAAATg                     <  1:3471693/71‑1 (MQ=255)
                                              aaCCGCTTAACGTACCGTTCTCATCCACACAAAGTc                                                        <  1:3275478/36‑1 (MQ=255)
                                              aaCCGCTTAACGTACCGTTCTCATCCACACAAAGTc                                                        <  1:908900/36‑1 (MQ=255)
                                              aaCCGCTTAACGTACCGTTCTCATCCACACAAAGTc                                                        <  1:2159766/36‑1 (MQ=255)
                                              aaCCGCTTAACGTACCGTTCTCATCCACACAAAGTc                                                        <  1:1292100/36‑1 (MQ=255)
                                              aaCCGCTTAACGTACCGTTCTCATCCACACAAAGTCCGTTACGGTAGTATATTg                                      <  1:1591649/54‑1 (MQ=255)
                                              aaCCGCTTAACGTACCGTTCTCATCCACACAAAGTCCGTTACGGTAGTATATTGTTTTACCCGCAAAAATg                     <  1:3986043/71‑1 (MQ=255)
                                                ccGCTTAACGTACCGTTCTCATCCACACAAAGTCCGTTACGGTAGTATATTGTTTTACCCGCaaa                         <  1:3943497/65‑1 (MQ=255)
                                                ccGCTTAACGTACCGTTCTCATCCACACAAAGTCCGTTACGGTAGTATATTGTTTTACCCGCaaa                         <  1:4227976/65‑1 (MQ=255)
                                                ccGCTTAACGTACCGTTCTCATCCACACAAAGTCCGTTACGGTAGTATATTGTTTTACCCGCaaa                         <  1:807294/65‑1 (MQ=255)
                                                 cGCTTAACGTACCGTTCTCATTCACACAAAGTCCGTTACGGTAGTATATTGTTTTACCCGCAAAAATGAAc                  >  1:1332772/1‑71 (MQ=255)
                                                 cGCTTAACGTACCGTTCTCATTCACACAAAGTCCGTTACGGTAGTATATTGTTTTACCCGCAAAAATGAAc                  >  1:2891023/1‑71 (MQ=255)
                                                 cGCTTAACGTACCGTTCTCATTCACACAAAGTCCGTTACGGTAGTATATTGTTTTACCCGCAAAAATGAAc                  >  1:4122764/1‑71 (MQ=255)
                                                  gCTTAACGTACCGTTCTCATCCACACAAAGTCCGTTACGGTAGTATATTGTTTTACCCGCAAAAATGAACt                 >  1:2859804/1‑71 (MQ=255)
                                                   cTTAACGTACCGTTCTCATTCACACAAAGTCCGTTACGgtag                                             <  1:3804887/42‑1 (MQ=255)
                                                     tAACGTACCGTTCTCATCCACACAAAGTCCGTTACGGTAGTATATTGTTTTACCCGCaaaaa                       >  1:4604941/1‑62 (MQ=255)
                                                     tAACGTACCGTTCTCATCCACACAAAGTCCGTTACGGTAGTATATTGTTTTACCCGCaaaaa                       >  1:1859927/1‑62 (MQ=255)
                                                     tAACGTACCGTTCTCATCCACACAAAGTCCGTTACGGTAGTATATTGTTTTACCCGCaaaaa                       >  1:3310257/1‑62 (MQ=255)
                                                     tAACGTACCGTTCTCATCCACACAAAGTCCGTTACGGTAGTATATTGTTTTACCCGCaaaaa                       >  1:2514048/1‑62 (MQ=255)
                                                        cGTACCGTTCTCATTCACACAAAGTCCGTTACGGTAGTATATTGTTTTACCCGCAAAAATGAACTGTTCaa           <  1:2320979/71‑1 (MQ=255)
                                                        cGTACCGTTCTCATTCACACAAAGTCCGTTACGGTAGTATATTGTTTTACCCGCAAAAATGAACTGTTCaa           <  1:1205411/71‑1 (MQ=255)
                                                        cGTACCGTTCTCATCCACACAAAGTCCGTTACGGTAGTATATTGTTTTACCCGCAAAAATGAACTGTTCaa           <  1:2191513/71‑1 (MQ=255)
                                                        cGTACCGTTCTCATCCACACAAAGTCCGTTACGGTAGTATATTGTTTTACCCGCAAAAATGAACTGTTCaa           <  1:1827699/71‑1 (MQ=255)
                                                         gTACCGTTCTCATCCACACAAAGTCCGTTACGGTAGTATATTGTTTTACCCGCAAAAATGAACTGTTCAAt          <  1:2752150/71‑1 (MQ=255)
                                                          tACCGTTCTCATTCACACAAAGTCCGTTACGgtagt                                            <  1:1836494/36‑1 (MQ=255)
                                                          tACCGTTCTCATCCACACAAAGTCCGTTACGGTAGTATATTGTTTTACCCGCAAAAATGAACTGTTCAATg         >  1:4199659/1‑71 (MQ=255)
                                                           aCCGTTCTCATCCACACAAAGTCCGTTACGgtagta                                           <  1:1255393/36‑1 (MQ=255)
                                                              gTTCTCATTCACACAAAGTCCGTTACGGTAGTATAtt                                       >  1:547253/1‑37 (MQ=255)
                                                                 ctcATTCACACAAAGTCCGTTACGGTAGTATATTGtt                                    >  1:1419816/1‑37 (MQ=255)
                                                                 ctcATCCACACAAAGTCCGTTACGGTAGTATATTGTTTTACCCGCAAAAATGAACTGTTc             <  1:3609443/60‑1 (MQ=255)
                                                                 ctcATCCACACAAAGTCCGTTACGGTAGTATATTGTTTTACCCGCAAAAATGAACTGTTCAATGTTGGCAc  >  1:2763738/1‑71 (MQ=255)
                                                                 ctcATCCACACAAAGTCCGTTACGGTAGTATATTGTTTTACCCGCAAAAATGAACTGTTCAATGTTGGCAc  >  1:3561500/1‑71 (MQ=255)
                                                                  tcATCCACACAAAGTCCGTTACGGTAGTATATTGTTTTACCCGCAAAAATGAACTGTTCaa           <  1:4152756/61‑1 (MQ=255)
                                                                  tcATCCACACAAAGTCCGTTACGGTAGTATATTGTTTTACCCGCAAAAATGAACTGTTCaa           <  1:1118434/61‑1 (MQ=255)
                                                                      |                                                                 
CAATGTTCGACCAGATTACGCACGCCTTCAATCATGGTTAAGGATGAACCGCTTAACGTACCGTTCTCATCCACACAAAGTCCGTTACGGTAGTATATTGTTTTACCCGCAAAAATGAACTGTTCAATGTTGGCAC  >  W3110S.gb/702203‑702338

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