BamQC report ----------------------------------- >>>>>>> Input bam file = SRR9716681.sorted.bam outfile = /home/luna/rawdata/yangyxdownload/SRP215441/SRP215441.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 = 588,811 number of mapped reads = 491,558 (83.48%) number of supplementary alignments = 1,848 (0.31%) number of secondary alignments = 0 number of mapped bases = 27,812,023 bp number of sequenced bases = 27,802,763 bp number of aligned bases = 0 bp number of duplicated reads (estimated) = 6,940 duplication rate = 0.98% >>>>>>> Insert size mean insert size = 0 std insert size = 0 median insert size = 0 >>>>>>> Mapping quality mean mapping quality = 41.6695 >>>>>>> ACTG content number of A's = 6,934,545 bp (24.94%) number of C's = 5,117,226 bp (18.41%) number of T's = 8,644,060 bp (31.09%) number of G's = 7,106,730 bp (25.56%) number of N's = 202 bp (0%) GC percentage = 43.97% >>>>>>> Mismatches and indels general error rate = 0.0054 number of mismatches = 146,855 number of insertions = 2,381 mapped reads with insertion percentage = 0.48% number of deletions = 5,682 mapped reads with deletion percentage = 1.14% homopolymer indels = 38.39% >>>>>>> Coverage mean coverageData = 0.009X std coverageData = 0.1114X There is a 0.86% of reference with a coverageData >= 1X There is a 0.03% of reference with a coverageData >= 2X There is a 0% of reference with a coverageData >= 3X There is a 0% of reference with a coverageData >= 4X There is a 0% 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 2326225 0.009332875443467802 0.13047379444546922 chr2 243199373 2149577 0.00883874400449215 0.14513782880638693 chr3 198022430 1595050 0.008054895599453053 0.0937458096443334 chr4 191154276 1690915 0.00884581310647741 0.10084680612502475 chr5 180915260 1580175 0.008734337833082736 0.09577880189693047 chr6 171115067 1609787 0.009407628610518559 0.10811494952906629 chr7 159138663 1568885 0.009858603625443304 0.13638954860479044 chr8 146364022 1419547 0.009698742768902592 0.10924796551063644 chr9 141213431 922158 0.0065302428633718275 0.08824614255305076 chr10 135534747 1223404 0.00902649709450522 0.12285861954036872 chr11 135006516 984356 0.007291174005260605 0.09660794661985232 chr12 133851895 1394034 0.010414749824797027 0.10538450935345814 chr13 115169878 823322 0.007148761588511885 0.08697270574119288 chr14 107349540 925735 0.008623558144729824 0.09716633840198335 chr15 102531392 1000807 0.009760981300244125 0.10293412579766788 chr16 90354753 969316 0.010727891647271727 0.11038322557736831 chr17 81195210 1231268 0.015164293558696381 0.12946838431154112 chr18 78077248 503728 0.0064516618208674565 0.11171577233343231 chr19 59128983 813522 0.013758430446875773 0.1404651648951144 chr20 63025520 876140 0.013901352975746968 0.1233873382947084 chr21 48129895 350089 0.0072738367702651335 0.09098176108099178 chr22 51304566 256377 0.004997157562935042 0.07296645512506143 chrMT 16571 26386 1.5922998008569187 1.6386657294114781 chrX 155270560 1481025 0.009538350347934599 0.10323375781494605 chrY 59373566 90195 0.0015191103731246327 0.05494118844033766