BamQC report ----------------------------------- >>>>>>> Input bam file = SRR10524979.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 = 1,657,828 number of mapped reads = 1,540,430 (92.92%) number of supplementary alignments = 3,795 (0.23%) number of secondary alignments = 0 number of mapped bases = 89,723,522 bp number of sequenced bases = 89,696,664 bp number of aligned bases = 0 bp number of duplicated reads (estimated) = 63,664 duplication rate = 3.2% >>>>>>> Insert size mean insert size = 0 std insert size = 0 median insert size = 0 >>>>>>> Mapping quality mean mapping quality = 45.8141 >>>>>>> ACTG content number of A's = 22,974,842 bp (25.61%) number of C's = 17,356,758 bp (19.35%) number of T's = 28,098,426 bp (31.33%) number of G's = 21,265,621 bp (23.71%) number of N's = 1,017 bp (0%) GC percentage = 43.06% >>>>>>> Mismatches and indels general error rate = 0.0049 number of mismatches = 426,172 number of insertions = 5,011 mapped reads with insertion percentage = 0.32% number of deletions = 15,601 mapped reads with deletion percentage = 1.01% homopolymer indels = 44.82% >>>>>>> Coverage mean coverageData = 0.029X std coverageData = 0.2544X There is a 2.58% of reference with a coverageData >= 1X There is a 0.23% of reference with a coverageData >= 2X There is a 0.03% of reference with a coverageData >= 3X There is a 0.01% 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 7051020 0.028288876359509652 0.41814587940724607 chr2 243199373 7349101 0.030218420834497793 0.29618975494729965 chr3 198022430 6126367 0.030937742759746964 0.1934096733178977 chr4 191154276 5830743 0.030502812293877225 0.21298721097841286 chr5 180915260 5406576 0.029884576900809805 0.19087509103748648 chr6 171115067 5246852 0.030662711893161342 0.23200388685868503 chr7 159138663 4821117 0.030295070406617657 0.2978801966902472 chr8 146364022 4640882 0.03170780589781825 0.2677524812618522 chr9 141213431 3816106 0.02702367595614896 0.2275876127056452 chr10 135534747 4386155 0.032361848877026346 0.26215172469652415 chr11 135006516 4179911 0.030960809328640107 0.25346768202593756 chr12 133851895 3786424 0.028288161329355854 0.18735852254277444 chr13 115169878 2743091 0.023817781590425927 0.17144377839757186 chr14 107349540 2741060 0.0255339706159896 0.1796938313330432 chr15 102531392 2609908 0.025454721223330316 0.18534975379782462 chr16 90354753 2662917 0.029471797681744533 0.19984116530382529 chr17 81195210 2430081 0.029928871419878093 0.2091353571871145 chr18 78077248 2440596 0.031258734939018346 0.3798920684953329 chr19 59128983 1753219 0.029650755197328526 0.30307813520440335 chr20 63025520 1926872 0.03057288539626488 0.19591580806454362 chr21 48129895 1183106 0.02458152048742263 0.18920353778875756 chr22 51304566 1061045 0.020681297645125777 0.15707408979865028 chrMT 16571 100441 6.061251584092692 4.054737230950839 chrX 155270560 5172624 0.03331361721114421 0.218157330083399 chrY 59373566 257308 0.004333713087066389 0.12417776936073638