BamQC report ----------------------------------- >>>>>>> Input bam file = SRR10524962.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 = 551,812 number of mapped reads = 511,725 (92.74%) number of supplementary alignments = 1,286 (0.23%) number of secondary alignments = 0 number of mapped bases = 29,924,504 bp number of sequenced bases = 29,914,526 bp number of aligned bases = 0 bp number of duplicated reads (estimated) = 8,565 duplication rate = 1.2% >>>>>>> Insert size mean insert size = 0 std insert size = 0 median insert size = 0 >>>>>>> Mapping quality mean mapping quality = 44.6932 >>>>>>> ACTG content number of A's = 7,730,177 bp (25.84%) number of C's = 5,306,981 bp (17.74%) number of T's = 9,274,334 bp (31%) number of G's = 7,602,667 bp (25.41%) number of N's = 367 bp (0%) GC percentage = 43.16% >>>>>>> Mismatches and indels general error rate = 0.0049 number of mismatches = 143,304 number of insertions = 1,614 mapped reads with insertion percentage = 0.31% number of deletions = 5,760 mapped reads with deletion percentage = 1.12% homopolymer indels = 45.59% >>>>>>> Coverage mean coverageData = 0.0097X std coverageData = 0.1207X There is a 0.92% 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 3299783 0.013238815561466544 0.19614280425994993 chr2 243199373 2599552 0.010688974925934534 0.13154643307136488 chr3 198022430 1723081 0.008701443568791677 0.09585851979734633 chr4 191154276 2003165 0.010479310439280992 0.10753909547334532 chr5 180915260 1344514 0.007431733508826177 0.0891679244733895 chr6 171115067 1824773 0.010664011252732059 0.12391308577143721 chr7 159138663 1953542 0.012275722085210682 0.15583635458418868 chr8 146364022 1886454 0.012888782189929162 0.12968477141729115 chr9 141213431 869717 0.006158883003133038 0.09496566891862064 chr10 135534747 1553330 0.011460751094330077 0.12333128515653814 chr11 135006516 1304348 0.0096613707148772 0.11754997849749883 chr12 133851895 1679671 0.012548727830861117 0.11512230366131283 chr13 115169878 614351 0.005334302776634009 0.0752206993346578 chr14 107349540 702843 0.006547238115785126 0.08474926589756247 chr15 102531392 862265 0.008409765859806136 0.09636866747290689 chr16 90354753 798637 0.008838904136011528 0.09848507747651301 chr17 81195210 769119 0.009472467649261575 0.11537270546706023 chr18 78077248 608998 0.007799941924182574 0.12857523927756875 chr19 59128983 733790 0.012409988516122458 0.1344858016655888 chr20 63025520 572893 0.009089857568807048 0.09822153072448023 chr21 48129895 439291 0.009127196309071524 0.10049765616553025 chr22 51304566 401850 0.007832636182908165 0.09113655260661141 chrMT 16571 2453 0.1480296904230282 0.36798131062550526 chrX 155270560 1299182 0.008367213977974962 0.09965943759651477 chrY 59373566 76902 0.0012952228606245412 0.04275583164968926