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 4,477,260 G→A 42.6% intergenic (‑45/+236) pyrL ← / ← yjgH pyrBI operon leader peptide/predicted mRNA endoribonuclease

Read alignment evidence...
  seq id position ref new freq score (cons/poly) reads annotation genes product
*W3110S.gb4,477,2600GA42.6% 38.8 / 83.2 68intergenic (‑45/+236)pyrL/yjgHpyrBI operon leader peptide/predicted mRNA endoribonuclease
Reads supporting (aligned to +/- strand):  ref base G (19/20);  new base A (17/12);  total (36/32)
Fisher's exact test for biased strand distribution p-value = 4.68e-01
Kolmogorov-Smirnov test that lower quality scores support variant p-value = 1.00e+00

ACAAAATGTCGAACACACTGAACCATACATCCTCCCGGCAAATTGTCCGGCATTATACTCATCGTCAGAAGCGGCGCAAGCATTTGATGCAATATTTTGTCAGCGCAAACGGTTTATTTGAATTAAAAGTCAAGGTATATG  >  W3110S.gb/4477190‑4477330
                                                                      |                                                                      
aCAAAATGTCGAACACACTGAACCATACATCCTCCCGGCAAATTGTCCGGCATTATACTCATCGTCAGAAg                                                                        <  1:1366111/71‑1 (MQ=255)
  aaaaTGTCGAACACACTGAACCATACATCCTCCCGGCAAATTGTCCGGCATTATACTCATCGTCAGAAgcg                                                                      >  1:4845669/1‑71 (MQ=255)
  aaaaTGTCGAACACACTGAACCATACATCCTCCCGGCAAATTGTCCGGCATTATACTCATCGTCAGAAgcg                                                                      >  1:4409327/1‑71 (MQ=255)
          gAACACACTGAACCATACATCCTCCCGGCAAATTGTCCGGCATTATACTCATCGTCAGAAACGGCGCAAGc                                                              <  1:254923/71‑1 (MQ=255)
          gAACACACTGAACCATACATCCTCCCGGCAAATTGTCCGGCATTATACTCATCGTCAGAAACGGCGCAAGc                                                              <  1:2827333/71‑1 (MQ=255)
            acacacTGAACCATACATCCTCCCGGCAAATTGTCCGGCATTATACTCATCGTCAGAAACGGCGCAAGCAt                                                            >  1:3476116/1‑71 (MQ=255)
               cacTGAACCATACATCCTCCCGGCAAATTGTCCGGCATTATACTCATCGTCAGAAGCGGCGCAAGCATTTg                                                         <  1:3504881/71‑1 (MQ=255)
                acTGAACCATACATCCTCCCGGCAAATTGTCCGGCATTATACTCATCGTCAGAAACGGCGCAAGCATTTGa                                                        >  1:3351540/1‑71 (MQ=255)
                 cTGAACCATACATCCTCCCGGCAAATTGTCCGGCATTATACTCATCGTCAGAAGCGGCGCAAGCATTTGa                                                        >  1:3323878/1‑70 (MQ=255)
                      ccATACATCCTCCCGGCAAATTGTCCGGCATTATACTCATCGTCAGAAGCGGCGCAAGCATTTGATGCaa                                                   >  1:1275365/1‑70 (MQ=255)
                         tACATCCTCCCGGCAAATTGTCCGGCATTATACTCATCGTCAGAAgcg                                                                      <  1:2874452/48‑1 (MQ=255)
                         tACATCCTCCCGGCAAATTGTCCGGCATTATACTCATCGTCAGAAGCGGCGCAAg                                                               <  1:2407021/55‑1 (MQ=255)
                         tACATCCTCCCGGCAAATTGTCCGGCATTATACTCATCGTCAGAAGCGGCGCAAGCATTTGATGCAATAtt                                               >  1:1688959/1‑71 (MQ=255)
                           cATCCTCCCGGCAAATTGTCCGGCATTATACTCATCGTCAGAAGCGGCGCAAGCATTTGa                                                        >  1:1774089/1‑60 (MQ=255)
                           cATCCTCCCGGCAAATTGTCCGGCATTATACTCATCGTCAGAAGCGGCGCAAGCATTTGATGCAATAtttt                                             >  1:3829387/1‑71 (MQ=255)
                             tcctccCGGCAAATTGTCCGGCATTATACTCATCGTCAGAAACGGCGCAAg                                                               <  1:2206481/51‑1 (MQ=255)
                               ctccCGGCAAATTGTCCGGCATTATACTCATCGTCAGAAGCGGCGCAAGCAttt                                                          <  1:1611998/54‑1 (MQ=255)
                               ctccCGGCAAATTGTCCGGCATTATACTCATCGTCAGAAACGGCGCAAGCATTTGATGCAATATTTTGt                                           >  1:4820524/1‑69 (MQ=255)
                               ctccCGGCAAATTGTCCGGCATTATACTCATCGTCAGAAACGGCGCAAGCATTTGATGCAATATTTTGt                                           >  1:1124691/1‑69 (MQ=255)
                               ctccCGGCAAATTGTCCGGCATTATACTCATCGTCAGAAACGGCGCAAGCATTTGATGCAATATTTTGt                                           >  1:4581817/1‑69 (MQ=255)
                               atccCGGCAAATTGTCCGGCATTATACTCATCGTCAGAAACGGCGCAAGCATTTGATGCAATATTTTGt                                           >  1:2047440/2‑69 (MQ=255)
                                 cccGGCAAATTGTCCGGCATTATACTCATCGTCAGAAGCGGCGCAAGCATTTGATGCAATATTTTGTCAg                                        >  1:3537143/1‑70 (MQ=255)
                                 cccGGCAAATTGTCCGGCATTATACTCATCGTCAGAAGAGGCGCAAGCATTTGATGCAATATTTTGTCAgc                                       >  1:2543330/1‑71 (MQ=255)
                                  ccGGCAAATTGTCCGGCATTATACTCATCGTCAGAAg                                                                        >  1:1097808/1‑37 (MQ=255)
                                  ccGGCAAATTGTCCGGCATTATACTCATCGTCAGAAg                                                                        >  1:14851/1‑37 (MQ=255)
                                     gCAAATTGTCCTGCATTATACTCATCGTCAGAAGCGGCGCAAGCAttt                                                          <  1:325986/48‑1 (MQ=255)
                                     gCAAATTGTCCGGCATTATACTCATCGTCAGAAGCGGCGCAAGCATTTGATGCAATATTTTGTCAGCGCaa                                   <  1:1243334/71‑1 (MQ=255)
                                        aaTTGTCCGGCATTATACTCATCGTCAGAAGCGGCGCAAGCATTTGATGCAATATTTTGTCAGCGCAAACg                                >  1:2225907/1‑71 (MQ=255)
                                        aaTTGTCCGGCATTATACTCATCGTCAGAAACGGCGCAAGCATTTGATGCAATATTTTGTCAGCGCAAACg                                <  1:3033652/71‑1 (MQ=255)
                                          ttGTCCGGCATTATACTCATCGTCAGAAACGGCGCAAGCAttt                                                          >  1:71022/1‑43 (MQ=255)
                                          ttGTCCGGCATTATACTCATCGTCAGAAACGGCGCAAGCATTTGATg                                                      >  1:49515/1‑47 (MQ=255)
                                          ttGTCCGGCATTATACTCATCGTCAGAAACGGCGCAAGCATTTGATGCaa                                                   >  1:2269044/1‑50 (MQ=255)
                                          ttGTCCGGCATTATACTCATCGTCAGAAACGGCGCAAGCATTTGATGCaa                                                   >  1:4246708/1‑50 (MQ=255)
                                          ttGTCCGGCATTATACTCATCGTCAGAAACGGCGCAAGCATTTGATGCAATATTTTGTCa                                         >  1:3492416/1‑60 (MQ=255)
                                           tGTCCGGCATTATACTCATCGTCAGAAGCGGCGCAAGCAttt                                                          <  1:2281010/42‑1 (MQ=255)
                                           tGTCCGGCATTATACTCATCGTCAGAAACGGCGCAAGCATTTGATGCAATATTTTGTCAGCGCAAACGGtt                             >  1:4134959/1‑71 (MQ=255)
                                            gTCCGGCATTATACTCATCGTCAGAAGCGGCGCAAGCATTTGa                                                        >  1:3628806/1‑43 (MQ=255)
                                            gTCCGGCATTATACTCATCGTCAGAAGCGGCGCAAGCATTTGa                                                        >  1:4655253/1‑43 (MQ=255)
                                            gTCCGGCATTATACTCATCGTCAGAAGCGGCGCAAGCATTTGa                                                        >  1:2276553/1‑43 (MQ=255)
                                            gTCCGGCATTATACTCATCGTCAGAAGCGGCGCAAGCATATGa                                                        >  1:2051336/1‑43 (MQ=255)
                                             tCCGGCATTATACTCATCGTCAGAAGCGGCGCAAGCATTTGATGCAATATTTTGTCAGCGCAAACGGTTTa                           <  1:395499/71‑1 (MQ=255)
                                              ccGGCATTATACTCATCGTCAGAAGCGGCGCAAGCATTTGATGCAATATTTTGTCAGCGCAAACGGt                              <  1:1810595/67‑1 (MQ=255)
                                              ccGGCATTATACTCATCGTCAGAAGCGGCGCAAGCATTTGATGCAATATTTTGTCAGCGCAAACGGTTTAt                          >  1:713281/1‑71 (MQ=255)
                                              ccGGCATCATACTCATCGTCAGAAGCGGCGCAAGCATTTGATGCAATATTTTGTCAGCGCAAACGGt                              <  1:165034/67‑1 (MQ=255)
                                                 gCATTATACTCATCGTCAGAAGCGGCGCAAGCATTTGATGCAATATTTTGTCAGCGCAAACGGTTTATTTg                       <  1:2957751/71‑1 (MQ=255)
                                                 gCATTATACTCATCGTCAGAAACGGCGCAAGCATTTGATGCAATATTTTGTCAGCGCAAACGGTTTa                           >  1:1244383/1‑67 (MQ=255)
                                                  cATTATACTCATCGTCAGAAACGGCGCAAGCATTTGATGCAATATTTTGTCAGCGCAAACGGTTTATTTGa                      <  1:440857/71‑1 (MQ=255)
                                                  cATTATACTCATCGTCAGAAACGGCGCAAGCATTTGATGCAATATTTTGTCAGCGCAAACGGGTTATTTGa                      <  1:4975935/71‑1 (MQ=255)
                                                     tataCTCATCGTCAGAAGCGGCGCAAGCATTTGATGCAATATTTTGTCAGCGCAAACGGTTTATTTGAAt                    >  1:1402540/1‑70 (MQ=255)
                                                      ataCTCATCGTCAGAAGCGGCGCAAGCATTTGATGCAATATTTTGTCAGCGCAAACGGTTTATTTGAAtt                   >  1:2448843/1‑70 (MQ=255)
                                                      ataCTCATCGTCAGAAACGGCGCAAGCATTTGATGCAat                                                  >  1:4068185/1‑39 (MQ=255)
                                                      ataCTCATCGTCAGAAACGGCGCAAGCATTTGATGCAATATTTTGt                                           <  1:4478388/46‑1 (MQ=255)
                                                      ataCTCATCGTCAGAAACGGCGCAAGCATTTGATGCAATATTTTGt                                           <  1:2176178/46‑1 (MQ=255)
                                                      ataCTCATCGTCAGAAACGGCGCAAGCATTTGATGCAATATTTTGTCAGCGCAAACGGTTTATTTGAAtt                   <  1:1773506/70‑1 (MQ=255)
                                                         cTCATCGTCAGAAGCGGCGCAAGCATTTGATGCAata                                                 <  1:1468244/37‑1 (MQ=255)
                                                         cTCATCGTCAGAAGCGGCGCAAGCATTTGATGCAATATTTTGTCAGCGTAAACGGTTTATTTGAATTaaa                <  1:4234892/70‑1 (MQ=255)
                                                         cTCATCGTCAGAAGCGGCGCAAGCATTTGATGCAATATTTTGTCAGCGCAAACGGTTTATTTGAATTaaa                <  1:1812069/70‑1 (MQ=255)
                                                         cTCATCGTCAGAAGCGGCGCAAGCATTTGATGCAATATTTTGTCAGCGCAAACGGTTTATTTGAATTaaa                <  1:24202/70‑1 (MQ=255)
                                                           cATCGTCAGAAGCGGCGCAAGCATTTGATGCAATAtt                                               >  1:4925299/1‑37 (MQ=255)
                                                           cATCGTCAGAAGCGGCGCAAGCATTTGATGCAATAtt                                               >  1:5121437/1‑37 (MQ=255)
                                                            aTCGTCAGAAACGGCGCAAGCATTTGATGCAATATTTTGTCAGCGCAAACGGTTTATTTg                       >  1:2082171/1‑60 (MQ=255)
                                                            aTCGTCAGAAACGGCGCAAGCATTTGATGCAATATTTTGTCAGCGCAAACGGTTTATTTGAATTAAAAGt             >  1:2074439/1‑70 (MQ=255)
                                                             tCGTCAGAAGCGGCGCAAGCATTTGATGCAATATTTTGTc                                          <  1:4017413/40‑1 (MQ=255)
                                                             tCGTCAGAAGCGGCGCAAGCATTTGATGCAATATTTTGTc                                          <  1:2484271/40‑1 (MQ=255)
                                                             tCGTCAGAAGCGGCGCAAGCATTTGATGCAATATTTTGTAAGCGCAAACGGTTTATTTg                       <  1:2219651/59‑1 (MQ=255)
                                                             tCGTCAGAAACGGCGCAAGCATTTGATGCAATATTTTGTCa                                         <  1:1024536/41‑1 (MQ=255)
                                                             tCGTCAGAAACGGCGCAAGCATTTGATGCAATATTTTGTCAGCGCAAACGGTTTATTTGAATTAAAAGTCa           <  1:178944/71‑1 (MQ=255)
                                                               gTCAGAAGCGGCGCAAGCATTTGATGCAATATTTTGTCAGCGCAAACGGTTTATTTGAATTaa                 <  1:2569229/63‑1 (MQ=255)
                                                               gTCAGAAACGGCGCAAGCATTTGATGCAATATTTTGTCAGCGCAAACGGTTTATTTGAATTAAAAGTCAAg         >  1:315002/1‑71 (MQ=255)
                                                                 cAGAAGCGGCGCAAGCATTTGATGCAATATTTTGTCAGCGCAAACGGTTTATTTGAATTAAAAGTCAAgg        >  1:3463994/1‑70 (MQ=255)
                                                                  aGAAGCGGCGCAAGCATTTGATGCAATATTTTGTCAGCGCAAACGGTTTATTTGAATTAAAAGTCAAGGta      >  1:859326/1‑71 (MQ=255)
                                                                  aGAAGCGGCGCAAGCATTTGATGCAATATTTTGTCAGCGCAAACGGTTTATTTGAATTAAAAGTCAAGGt       <  1:500462/70‑1 (MQ=255)
                                                                  aGAAACGGCGCAAGCATTTGATGCAATATTTTGTCAGCGCAAACGGTTTATTTGAATTAAAAGTCAAGGt       <  1:4033791/70‑1 (MQ=255)
                                                                     aGCGGCGCAAGCATTTGATGCAATATTTTGTCAGCGCAAACGGTTTATTTGAATTAAAAGTCAAGGTatat   <  1:4583771/71‑1 (MQ=255)
                                                                      gcggcgCAAGCATTTGATGCAATATTTTGTCAGCGCAAACGGTTTATTTGAATTAAAAGTCAAGGTATATg  >  1:1348462/1‑71 (MQ=255)
                                                                      gcggcgCAAGCATTTGATGCAATATTTTGTCAGCGCAAACGGTTTATTTGAATTAAAAGTCAAGGTATATg  >  1:4320019/1‑71 (MQ=255)
                                                                      gcggcgCAAGCATTTGATGCAATATTTTGTCAGCGCAAACGGTTTATTTGAATTAAAAGTCAAGGTATATg  >  1:3459505/1‑71 (MQ=255)
                                                                      |                                                                      
ACAAAATGTCGAACACACTGAACCATACATCCTCCCGGCAAATTGTCCGGCATTATACTCATCGTCAGAAGCGGCGCAAGCATTTGATGCAATATTTTGTCAGCGCAAACGGTTTATTTGAATTAAAAGTCAAGGTATATG  >  W3110S.gb/4477190‑4477330

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