BamQC report ----------------------------------- >>>>>>> Input bam file = SRR9716278.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 = 1,633,801 number of mapped reads = 1,216,175 (74.44%) number of supplementary alignments = 1,164 (0.07%) number of secondary alignments = 0 number of mapped bases = 62,864,644 bp number of sequenced bases = 62,848,986 bp number of aligned bases = 0 bp number of duplicated reads (estimated) = 96,973 duplication rate = 6.82% >>>>>>> Insert size mean insert size = 0 std insert size = 0 median insert size = 0 >>>>>>> Mapping quality mean mapping quality = 43.0144 >>>>>>> ACTG content number of A's = 12,064,273 bp (19.2%) number of C's = 10,136,977 bp (16.13%) number of T's = 21,743,920 bp (34.6%) number of G's = 18,902,826 bp (30.08%) number of N's = 990 bp (0%) GC percentage = 46.21% >>>>>>> Mismatches and indels general error rate = 0.0071 number of mismatches = 441,220 number of insertions = 3,787 mapped reads with insertion percentage = 0.31% number of deletions = 9,208 mapped reads with deletion percentage = 0.75% homopolymer indels = 41% >>>>>>> Coverage mean coverageData = 0.0203X std coverageData = 0.1901X There is a 1.74% of reference with a coverageData >= 1X There is a 0.21% 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 5144156 0.020638488198591088 0.19645947419302512 chr2 243199373 5163285 0.021230667399788076 0.28882061719651025 chr3 198022430 4037832 0.020390780983750176 0.1656346265618274 chr4 191154276 3723911 0.019481180740105443 0.17219525194012797 chr5 180915260 3669935 0.020285381122631667 0.16365801350331038 chr6 171115067 3507852 0.020499959831123463 0.19283897852334125 chr7 159138663 3389764 0.02130069422538758 0.20269145683743447 chr8 146364022 3042906 0.0207899862166947 0.1747399825839571 chr9 141213431 2634694 0.018657531237237623 0.1706622836635316 chr10 135534747 3063178 0.022600684088782044 0.19966697489192045 chr11 135006516 2901483 0.021491429347010184 0.18645230047628597 chr12 133851895 2869050 0.02143451162943939 0.17315612534299363 chr13 115169878 1900481 0.01650154565588756 0.15183793629031628 chr14 107349540 1898437 0.01768463097280156 0.15540566630837394 chr15 102531392 1867583 0.018214743441696372 0.1593776409102128 chr16 90354753 2037997 0.02255550408067631 0.19162875536466983 chr17 81195210 1999387 0.024624445210499488 0.1910972970359399 chr18 78077248 1614671 0.020680429207750765 0.1994029270081979 chr19 59128983 1578542 0.026696586342437177 0.22173143055355246 chr20 63025520 1501377 0.023821731260606816 0.18763383625105964 chr21 48129895 864723 0.017966442685985497 0.17227425376504926 chr22 51304566 934774 0.01822009370472016 0.16377273383367624 chrMT 16571 21945 1.3243014905557902 1.5762697726439994 chrX 155270560 3289428 0.021185136448274546 0.17256234865542322 chrY 59373566 207253 0.0034906611470835354 0.09538646992247349