BamQC report ----------------------------------- >>>>>>> Input bam file = SRR9716734.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 = 796,234 number of mapped reads = 737,843 (92.67%) number of supplementary alignments = 4,938 (0.62%) number of secondary alignments = 0 number of mapped bases = 43,555,621 bp number of sequenced bases = 43,543,700 bp number of aligned bases = 0 bp number of duplicated reads (estimated) = 16,147 duplication rate = 1.66% >>>>>>> Insert size mean insert size = 0 std insert size = 0 median insert size = 0 >>>>>>> Mapping quality mean mapping quality = 45.2505 >>>>>>> ACTG content number of A's = 11,292,603 bp (25.93%) number of C's = 8,899,117 bp (20.44%) number of T's = 13,210,550 bp (30.34%) number of G's = 10,140,849 bp (23.29%) number of N's = 581 bp (0%) GC percentage = 43.73% >>>>>>> Mismatches and indels general error rate = 0.0049 number of mismatches = 206,591 number of insertions = 3,012 mapped reads with insertion percentage = 0.41% number of deletions = 7,473 mapped reads with deletion percentage = 1.01% homopolymer indels = 41.35% >>>>>>> Coverage mean coverageData = 0.0141X std coverageData = 0.1525X There is a 1.31% of reference with a coverageData >= 1X There is a 0.06% of reference with a coverageData >= 2X There is a 0.01% 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 3844272 0.015423319647416245 0.204690678639279 chr2 243199373 4296648 0.017667183706102728 0.17698270503943944 chr3 198022430 3090419 0.01560640882954522 0.13228287740541383 chr4 191154276 2479143 0.01296933059451937 0.12788957875556617 chr5 180915260 2374671 0.013125874511636 0.11995838187660411 chr6 171115067 2369000 0.013844485126490936 0.12729692139097115 chr7 159138663 2036699 0.012798266377291357 0.23302811180269326 chr8 146364022 3550561 0.024258427388665228 0.19258463249683155 chr9 141213431 1787774 0.012660084719561837 0.12566141078553886 chr10 135534747 2048889 0.015117075475855649 0.18401390554381644 chr11 135006516 1474210 0.010919547023937718 0.1198541178755858 chr12 133851895 1948969 0.014560638084354352 0.13087290036752133 chr13 115169878 1059424 0.009198794149977306 0.10026162674186545 chr14 107349540 1401054 0.013051327467262551 0.12177542361391346 chr15 102531392 991179 0.009667078351964635 0.10266900111624527 chr16 90354753 1349446 0.014934975252491697 0.13063210004627396 chr17 81195210 1858471 0.02288892411264162 0.1618780240832045 chr18 78077248 957964 0.012269438594966871 0.16408932050922567 chr19 59128983 855730 0.014472259737665367 0.17952537495702933 chr20 63025520 1024563 0.01625631966225745 0.1353279342816562 chr21 48129895 443609 0.009216911859043117 0.10562142914993203 chr22 51304566 660590 0.012875852024554695 0.11856797630928168 chrMT 16571 95552 5.766218091847203 4.348338444114168 chrX 155270560 1457615 0.009387581264600322 0.10803072956594445 chrY 59373566 99169 0.001670255076139439 0.06058602931194966