BamQC report ----------------------------------- >>>>>>> Input bam file = SRR6231743.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 = 1,472,016 number of mapped reads = 857,244 (58.24%) number of supplementary alignments = 6,516 (0.44%) number of secondary alignments = 0 number of mapped bases = 55,765,886 bp number of sequenced bases = 55,732,045 bp number of aligned bases = 0 bp number of duplicated reads (estimated) = 63,115 duplication rate = 5.73% >>>>>>> Insert size mean insert size = 0 std insert size = 0 median insert size = 0 >>>>>>> Mapping quality mean mapping quality = 44.2462 >>>>>>> ACTG content number of A's = 15,876,310 bp (28.49%) number of C's = 9,454,935 bp (16.96%) number of T's = 18,648,386 bp (33.46%) number of G's = 11,750,982 bp (21.08%) number of N's = 1,432 bp (0%) GC percentage = 38.05% >>>>>>> Mismatches and indels general error rate = 0.009 number of mismatches = 492,966 number of insertions = 5,111 mapped reads with insertion percentage = 0.59% number of deletions = 19,199 mapped reads with deletion percentage = 2.21% homopolymer indels = 44% >>>>>>> Coverage mean coverageData = 0.018X std coverageData = 0.376X There is a 1.41% of reference with a coverageData >= 1X There is a 0.27% of reference with a coverageData >= 2X There is a 0.07% 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% 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 5123187 0.020554360023038818 0.33495716853037094 chr2 243199373 1368415 0.005626720920863558 0.16451792527370282 chr3 198022430 8829016 0.04458593907770953 0.2659994592829213 chr4 191154276 798574 0.004177641309996121 0.08353330678191291 chr5 180915260 2097977 0.011596462343751434 0.13206742629600995 chr6 171115067 2822045 0.016492089501387974 0.16712579094377578 chr7 159138663 3686917 0.023167952592387936 0.25045130844022806 chr8 146364022 3329123 0.022745500940114915 1.4439356872207572 chr9 141213431 907009 0.006422965532223348 0.13599193436063609 chr10 135534747 2048663 0.015115408006774824 0.2335641905559545 chr11 135006516 2810778 0.020819572886393127 0.19136308116301545 chr12 133851895 2147579 0.016044442254627773 0.19497080674226122 chr13 115169878 3137435 0.02724180188851116 0.20845671259149365 chr14 107349540 3157942 0.029417378034409837 0.21975874491761535 chr15 102531392 325093 0.0031706679647926753 0.07636539099123638 chr16 90354753 2248642 0.024886814753397643 0.2034013945923788 chr17 81195210 1232295 0.01517694208808623 0.1499523150991691 chr18 78077248 1772137 0.02269722672602395 0.3976803275056194 chr19 59128983 1073834 0.018160873830689764 0.25888913900203603 chr20 63025520 1335151 0.021184291696442963 0.18947417625216884 chr21 48129895 1432677 0.02976688397097064 0.21714636525194206 chr22 51304566 585664 0.011415436201136562 0.12769529886671968 chrMT 16571 65034 3.9245670146641722 3.1629682986029524 chrX 155270560 3243563 0.02088974883583855 0.18987097247673296 chrY 59373566 187136 0.0031518403324469345 0.07291649204246628