BamQC report ----------------------------------- >>>>>>> Input bam file = SRR10525214.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 = 2,130,335 number of mapped reads = 1,967,187 (92.34%) number of supplementary alignments = 5,998 (0.28%) number of secondary alignments = 0 number of mapped bases = 114,465,729 bp number of sequenced bases = 114,429,446 bp number of aligned bases = 0 bp number of duplicated reads (estimated) = 78,762 duplication rate = 2.87% >>>>>>> Insert size mean insert size = 0 std insert size = 0 median insert size = 0 >>>>>>> Mapping quality mean mapping quality = 44.8213 >>>>>>> ACTG content number of A's = 27,474,255 bp (24.01%) number of C's = 20,083,116 bp (17.55%) number of T's = 37,980,368 bp (33.19%) number of G's = 28,889,033 bp (25.25%) number of N's = 2,674 bp (0%) GC percentage = 42.8% >>>>>>> Mismatches and indels general error rate = 0.0052 number of mismatches = 579,484 number of insertions = 6,738 mapped reads with insertion percentage = 0.34% number of deletions = 22,736 mapped reads with deletion percentage = 1.15% homopolymer indels = 45.46% >>>>>>> Coverage mean coverageData = 0.037X std coverageData = 0.3338X There is a 3.28% of reference with a coverageData >= 1X There is a 0.29% 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 11854304 0.047559777193092734 0.5785267986310292 chr2 243199373 9368712 0.03852276379018461 0.454201308165098 chr3 198022430 10661356 0.053839133273942755 0.2610935273001395 chr4 191154276 5819779 0.030445455481205138 0.2097895869054763 chr5 180915260 5116949 0.028283678225927433 0.18689369097088 chr6 171115067 7158565 0.04183480230878792 0.2631902564232878 chr7 159138663 6731424 0.04229911118456487 0.5266732354103006 chr8 146364022 6432170 0.043946387316413045 0.3210298926940374 chr9 141213431 3768129 0.026683927819868634 0.24957550551027413 chr10 135534747 6028893 0.044482268447367225 0.3810336862775673 chr11 135006516 5093936 0.03773103810781992 0.27002530083595344 chr12 133851895 4872689 0.03640358621743831 0.21389850710255398 chr13 115169878 3460230 0.030044574676027704 0.19379385741986802 chr14 107349540 4211026 0.03922723842132905 0.22422861366522556 chr15 102531392 3078451 0.030024472895091487 0.19787255893539488 chr16 90354753 3021228 0.033437399801203596 0.22849480261630137 chr17 81195210 2135183 0.026296908401369983 0.1870921069830181 chr18 78077248 2620253 0.033559750978927945 0.4717940501996797 chr19 59128983 1686772 0.028526991577040993 0.3985324848311868 chr20 63025520 2036421 0.03231105431577558 0.20206325853975407 chr21 48129895 1475388 0.030654295007292245 0.20969205124847037 chr22 51304566 950128 0.018519365313410897 0.15045895048307406 chrMT 16571 167177 10.088528151590127 5.944674566423078 chrX 155270560 6366370 0.04100178424036083 0.2474058580207507 chrY 59373566 350196 0.005898180345105092 0.1617918526302419