BamQC report ----------------------------------- >>>>>>> Input bam file = SRR6003989.sorted.bam outfile = /home/luna/rawdata/yangyxdownload/SRP116771/SRP116771.result/quality.files/genome_results.txt >>>>>>> Reference number of bases = 3,095,693,983 bp number of contigs = 25 >>>>>>> Globals number of windows = 424 number of reads = 2,994,538 number of mapped reads = 2,353,523 (78.59%) number of supplementary alignments = 15,651 (0.52%) number of secondary alignments = 0 number of mapped bases = 157,772,916 bp number of sequenced bases = 157,701,983 bp number of aligned bases = 0 bp number of duplicated reads (estimated) = 97,462 duplication rate = 2.8% >>>>>>> Insert size mean insert size = 0 std insert size = 0 median insert size = 0 >>>>>>> Mapping quality mean mapping quality = 44.5004 >>>>>>> ACTG content number of A's = 44,659,029 bp (28.32%) number of C's = 27,991,017 bp (17.75%) number of T's = 50,874,257 bp (32.26%) number of G's = 34,160,935 bp (21.66%) number of N's = 16,745 bp (0.01%) GC percentage = 39.41% >>>>>>> Mismatches and indels general error rate = 0.0103 number of mismatches = 1,601,939 number of insertions = 14,783 mapped reads with insertion percentage = 0.62% number of deletions = 42,789 mapped reads with deletion percentage = 1.8% homopolymer indels = 46.59% >>>>>>> Coverage mean coverageData = 0.051X std coverageData = 0.5616X There is a 4.44% of reference with a coverageData >= 1X There is a 0.45% of reference with a coverageData >= 2X There is a 0.06% of reference with a coverageData >= 3X There is a 0.02% of reference with a coverageData >= 4X There is a 0.01% of reference with a coverageData >= 5X There is a 0.01% of reference with a coverageData >= 6X There is a 0% of reference with a coverageData >= 7X There is a 0% of reference with a coverageData >= 8X There is a 0% of reference with a coverageData >= 9X There is a 0% of reference with a coverageData >= 10X There is a 0% of reference with a coverageData >= 11X There is a 0% of reference with a coverageData >= 12X There is a 0% of reference with a coverageData >= 13X There is a 0% of reference with a coverageData >= 14X There is a 0% of reference with a coverageData >= 15X There is a 0% of reference with a coverageData >= 16X There is a 0% of reference with a coverageData >= 17X There is a 0% of reference with a coverageData >= 18X There is a 0% of reference with a coverageData >= 19X There is a 0% of reference with a coverageData >= 20X There is a 0% of reference with a coverageData >= 21X There is a 0% of reference with a coverageData >= 22X There is a 0% of reference with a coverageData >= 23X There is a 0% of reference with a coverageData >= 24X There is a 0% of reference with a coverageData >= 25X There is a 0% of reference with a coverageData >= 26X There is a 0% of reference with a coverageData >= 27X There is a 0% of reference with a coverageData >= 28X There is a 0% of reference with a coverageData >= 29X There is a 0% of reference with a coverageData >= 30X There is a 0% of reference with a coverageData >= 31X There is a 0% of reference with a coverageData >= 32X There is a 0% of reference with a coverageData >= 33X There is a 0% of reference with a coverageData >= 34X There is a 0% of reference with a coverageData >= 35X There is a 0% of reference with a coverageData >= 36X There is a 0% of reference with a coverageData >= 37X There is a 0% of reference with a coverageData >= 38X There is a 0% of reference with a coverageData >= 39X There is a 0% of reference with a coverageData >= 40X There is a 0% of reference with a coverageData >= 41X There is a 0% of reference with a coverageData >= 42X There is a 0% of reference with a coverageData >= 43X There is a 0% of reference with a coverageData >= 44X There is a 0% of reference with a coverageData >= 45X There is a 0% of reference with a coverageData >= 46X There is a 0% of reference with a coverageData >= 47X There is a 0% of reference with a coverageData >= 48X There is a 0% of reference with a coverageData >= 49X There is a 0% of reference with a coverageData >= 50X There is a 0% of reference with a coverageData >= 51X >>>>>>> Coverage per contig chr1 249250621 12519002 0.05022656292599568 1.09933396187606 chr2 243199373 12917806 0.05311611555840648 0.5768520062233174 chr3 198022430 10911900 0.05510436368243739 0.2599313749430547 chr4 191154276 10578923 0.055342329878092816 0.2676220873299658 chr5 180915260 8560043 0.047315207130675434 0.24662087749009032 chr6 171115067 10057114 0.05877398277265672 0.3254885967196286 chr7 159138663 10067635 0.06326328756450593 0.8084786166393605 chr8 146364022 11210018 0.07658998329521172 1.0779550089414582 chr9 141213431 5137291 0.036379620292633495 0.47019687048403436 chr10 135534747 7781000 0.05740963238010102 0.4482825010973251 chr11 135006516 6960733 0.051558496628414587 0.4132101041132409 chr12 133851895 6960691 0.05200293204664753 0.2679701316623297 chr13 115169878 5091709 0.04421042279822507 0.23109440165104417 chr14 107349540 3939712 0.0366998498549691 0.2613105012751305 chr15 102531392 4422564 0.043133755562394 0.23660550299645566 chr16 90354753 3471184 0.03841728171178776 0.2769986924147425 chr17 81195210 3389193 0.04174129237426691 0.2584626364075729 chr18 78077248 4522412 0.05792227717862187 1.0118893346202924 chr19 59128983 2462580 0.041647596069764974 0.7230555911807206 chr20 63025520 3427372 0.05438070165862971 0.28035786759789383 chr21 48129895 1742297 0.03619989197981836 0.23751290467227634 chr22 51304566 1532973 0.02987985513803976 0.18720788676838052 chrMT 16571 152163 9.182487478124434 7.034989181130927 chrX 155270560 9581566 0.061708839074194104 0.33660606117603764 chrY 59373566 375035 0.006316531501577655 0.1162626565196685