BamQC report ----------------------------------- >>>>>>> Input bam file = SRR10524620.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 = 1,828,900 number of mapped reads = 1,699,946 (92.95%) number of supplementary alignments = 3,875 (0.21%) number of secondary alignments = 0 number of mapped bases = 98,914,750 bp number of sequenced bases = 98,882,744 bp number of aligned bases = 0 bp number of duplicated reads (estimated) = 80,901 duplication rate = 3.7% >>>>>>> Insert size mean insert size = 0 std insert size = 0 median insert size = 0 >>>>>>> Mapping quality mean mapping quality = 45.2896 >>>>>>> ACTG content number of A's = 25,235,778 bp (25.52%) number of C's = 19,002,191 bp (19.22%) number of T's = 31,187,305 bp (31.54%) number of G's = 23,456,859 bp (23.72%) number of N's = 611 bp (0%) GC percentage = 42.94% >>>>>>> Mismatches and indels general error rate = 0.0049 number of mismatches = 471,440 number of insertions = 5,934 mapped reads with insertion percentage = 0.35% number of deletions = 18,949 mapped reads with deletion percentage = 1.11% homopolymer indels = 44.56% >>>>>>> Coverage mean coverageData = 0.032X std coverageData = 0.2804X There is a 2.8% 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 10162197 0.04077099972400871 0.4882215874571153 chr2 243199373 8844990 0.036369296067223 0.33381487453282693 chr3 198022430 6378656 0.032211785301291374 0.2020832654402249 chr4 191154276 4482260 0.023448389927725185 0.19289232296782552 chr5 180915260 6182978 0.03417609990445251 0.20722016896124373 chr6 171115067 6491892 0.03793875147183854 0.23232811214278726 chr7 159138663 6077282 0.03818859531325835 0.36777599879675993 chr8 146364022 8867812 0.060587375769162725 0.36555490789466755 chr9 141213431 3603623 0.025518981972755834 0.23982963374327845 chr10 135534747 4259657 0.031428523639034055 0.2751983478053827 chr11 135006516 5078254 0.03761488075138536 0.28116767663832715 chr12 133851895 3020025 0.02256243738648601 0.17553348710304661 chr13 115169878 2447046 0.0212472743958277 0.16603366385083676 chr14 107349540 1811958 0.016879047641936797 0.1526153949886601 chr15 102531392 2543672 0.024808714193600336 0.18382922042379948 chr16 90354753 2929587 0.0324231642800241 0.21280548553180426 chr17 81195210 2137385 0.026324028227773535 0.1871461289989837 chr18 78077248 2647384 0.03390724017321922 0.4043034144994483 chr19 59128983 1975992 0.03341833225847974 0.35285374397680686 chr20 63025520 1825123 0.028958475868187998 0.1953038712991411 chr21 48129895 867335 0.018020712490646407 0.16590755067129792 chr22 51304566 1497454 0.02918753859061979 0.1900762068065052 chrMT 16571 5362 0.3235773338965663 0.6530441168322045 chrX 155270560 4541757 0.029250599727340457 0.21916795996305843 chrY 59373566 235069 0.0039591524618885114 0.1148232934125145