BamQC report ----------------------------------- >>>>>>> Input bam file = SRR10525166.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 = 492,150 number of mapped reads = 435,312 (88.45%) number of supplementary alignments = 1,487 (0.3%) number of secondary alignments = 0 number of mapped bases = 27,040,297 bp number of sequenced bases = 27,030,973 bp number of aligned bases = 0 bp number of duplicated reads (estimated) = 6,581 duplication rate = 1.14% >>>>>>> Insert size mean insert size = 0 std insert size = 0 median insert size = 0 >>>>>>> Mapping quality mean mapping quality = 45.8236 >>>>>>> ACTG content number of A's = 7,359,821 bp (27.23%) number of C's = 5,240,112 bp (19.39%) number of T's = 7,936,288 bp (29.36%) number of G's = 6,494,082 bp (24.02%) number of N's = 670 bp (0%) GC percentage = 43.41% >>>>>>> Mismatches and indels general error rate = 0.0049 number of mismatches = 129,884 number of insertions = 1,966 mapped reads with insertion percentage = 0.45% number of deletions = 5,679 mapped reads with deletion percentage = 1.29% homopolymer indels = 42.51% >>>>>>> Coverage mean coverageData = 0.0087X std coverageData = 0.1175X There is a 0.83% 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 2937452 0.01178513412811116 0.19171024766834735 chr2 243199373 2225913 0.00915262639266755 0.11783666032511689 chr3 198022430 2071950 0.010463208637526568 0.10515352654660397 chr4 191154276 1481108 0.007748233683247557 0.09253897784843758 chr5 180915260 1191548 0.006586221637688274 0.08317948419805983 chr6 171115067 1666923 0.009741532579360765 0.1052557416747082 chr7 159138663 1987003 0.012485985256769437 0.18427202339583512 chr8 146364022 1537176 0.010502417048911104 0.11211727089855376 chr9 141213431 898292 0.006361236276455884 0.09084310618065747 chr10 135534747 1495910 0.011037095896892035 0.1294687249408333 chr11 135006516 1241037 0.009192422979050877 0.10605949633591089 chr12 133851895 1224075 0.009144995668533494 0.09839419063898659 chr13 115169878 665922 0.00578208479130281 0.07764814776662021 chr14 107349540 1016385 0.00946799585727149 0.10074939373006958 chr15 102531392 736612 0.007184258261118702 0.08686909308553273 chr16 90354753 841685 0.009315337290557366 0.10220189492062147 chr17 81195210 513902 0.0063292157259030426 0.08290416890747938 chr18 78077248 582999 0.007466951191722331 0.14512012611791175 chr19 59128983 487608 0.008246514234821187 0.13700662280306575 chr20 63025520 438934 0.006964385220463076 0.0857002116532504 chr21 48129895 349846 0.0072687879331546435 0.08940169511496852 chr22 51304566 227689 0.004437987059475369 0.06814290494729504 chrMT 16571 73341 4.4258644620119485 3.1596746145651364 chrX 155270560 1072766 0.0069090109548133275 0.08719366060504147 chrY 59373566 74221 0.0012500680858549072 0.04790510524842659