BamQC report ----------------------------------- >>>>>>> Input bam file = SRR10524743.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 = 1,932,966 number of mapped reads = 1,762,095 (91.16%) number of supplementary alignments = 6,175 (0.32%) number of secondary alignments = 0 number of mapped bases = 101,341,197 bp number of sequenced bases = 101,307,251 bp number of aligned bases = 0 bp number of duplicated reads (estimated) = 71,661 duplication rate = 3.07% >>>>>>> Insert size mean insert size = 0 std insert size = 0 median insert size = 0 >>>>>>> Mapping quality mean mapping quality = 44.6715 >>>>>>> ACTG content number of A's = 23,554,095 bp (23.25%) number of C's = 18,902,409 bp (18.66%) number of T's = 32,671,884 bp (32.25%) number of G's = 26,167,117 bp (25.83%) number of N's = 11,746 bp (0.01%) GC percentage = 44.49% >>>>>>> Mismatches and indels general error rate = 0.0053 number of mismatches = 521,757 number of insertions = 6,598 mapped reads with insertion percentage = 0.37% number of deletions = 20,992 mapped reads with deletion percentage = 1.18% homopolymer indels = 43.39% >>>>>>> Coverage mean coverageData = 0.0327X std coverageData = 0.2755X There is a 2.9% of reference with a coverageData >= 1X There is a 0.27% of reference with a coverageData >= 2X There is a 0.04% of reference with a coverageData >= 3X There is a 0.01% 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 8150976 0.03270192855407169 0.3850865245270491 chr2 243199373 8486972 0.03489717878507853 0.4285642194477496 chr3 198022430 6664952 0.033657560913680336 0.20673067518798496 chr4 191154276 6378838 0.03337010363294201 0.23241951915663234 chr5 180915260 5972937 0.03301510884156483 0.2011644641813897 chr6 171115067 5793905 0.03385970096952363 0.22395743482336214 chr7 159138663 5641472 0.03545004019544892 0.33818639078131174 chr8 146364022 5054488 0.034533677955365286 0.25765696808550637 chr9 141213431 4358968 0.030867942016082027 0.24380735380849117 chr10 135534747 4934888 0.03641050069617941 0.32957684952636607 chr11 135006516 4542137 0.03364383538347142 0.24741024276901014 chr12 133851895 4614892 0.03447759928987184 0.2097746887530747 chr13 115169878 3128825 0.027167042757482125 0.18301892186148447 chr14 107349540 3074382 0.02863898624996437 0.19343301311727867 chr15 102531392 2944440 0.02871744879851041 0.18773039899544022 chr16 90354753 3072852 0.034008747719115565 0.22590564785777545 chr17 81195210 2937376 0.03617671535057302 0.22428041150986416 chr18 78077248 2672557 0.03422965163936106 0.37839411132289397 chr19 59128983 2222882 0.03759378036317655 0.3164302632267737 chr20 63025520 2203769 0.03496629619239952 0.21755497580800326 chr21 48129895 1348591 0.028019820113881405 0.20741109011199615 chr22 51304566 1289718 0.02513846428405612 0.176838555219691 chrMT 16571 15008 0.9056785951360811 1.0955552411901464 chrX 155270560 5503440 0.03544419495878678 0.22802713743725594 chrY 59373566 331932 0.0055905687052719725 0.1478157558430641