BamQC report ----------------------------------- >>>>>>> Input bam file = SRR10524901.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 = 3,407,153 number of mapped reads = 3,144,871 (92.3%) number of supplementary alignments = 10,853 (0.32%) number of secondary alignments = 0 number of mapped bases = 182,143,224 bp number of sequenced bases = 182,083,523 bp number of aligned bases = 0 bp number of duplicated reads (estimated) = 258,864 duplication rate = 6.13% >>>>>>> Insert size mean insert size = 0 std insert size = 0 median insert size = 0 >>>>>>> Mapping quality mean mapping quality = 44.6898 >>>>>>> ACTG content number of A's = 46,197,860 bp (25.37%) number of C's = 32,282,619 bp (17.73%) number of T's = 57,502,498 bp (31.58%) number of G's = 46,098,939 bp (25.32%) number of N's = 1,607 bp (0%) GC percentage = 43.05% >>>>>>> Mismatches and indels general error rate = 0.0051 number of mismatches = 906,425 number of insertions = 12,357 mapped reads with insertion percentage = 0.39% number of deletions = 35,636 mapped reads with deletion percentage = 1.12% homopolymer indels = 43.01% >>>>>>> Coverage mean coverageData = 0.0588X std coverageData = 0.5024X There is a 4.69% of reference with a coverageData >= 1X There is a 0.81% of reference with a coverageData >= 2X There is a 0.18% of reference with a coverageData >= 3X There is a 0.05% of reference with a coverageData >= 4X There is a 0.02% of reference with a coverageData >= 5X There is a 0.01% of reference with a coverageData >= 6X There is a 0.01% of reference with a coverageData >= 7X There is a 0.01% 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 17930038 0.0719357806534813 0.972183071400052 chr2 243199373 15800489 0.06496928345288128 0.6053518166262192 chr3 198022430 11148862 0.056301005901200185 0.29972241358438506 chr4 191154276 8355997 0.04371336689324177 0.3558628318289242 chr5 180915260 11032054 0.06097912359631796 0.30074499290090767 chr6 171115067 11742517 0.06862351285524144 0.3546844379226021 chr7 159138663 11645336 0.07317728941834832 0.6581008671148925 chr8 146364022 16290640 0.11130221605962701 0.6461835349054484 chr9 141213431 6613577 0.046833909162648985 0.38392758837419144 chr10 135534747 8021265 0.059182351223926365 0.5886282622261451 chr11 135006516 9393156 0.06957557515223932 0.421832461961315 chr12 133851895 6204326 0.0463521715549862 0.2840762168798528 chr13 115169878 4499224 0.03906597869279674 0.2417670880317887 chr14 107349540 3429180 0.03194405863313434 0.2307425556110124 chr15 102531392 4504399 0.04393190136343804 0.2647949382791906 chr16 90354753 5401979 0.059786329115414656 0.3425892987414642 chr17 81195210 4172023 0.051382624664681575 0.2916825339835898 chr18 78077248 4772333 0.06112322247833325 0.6806587320119342 chr19 59128983 3793463 0.06415572884113363 0.7132847314265318 chr20 63025520 3498973 0.05551676527222624 0.3002580499630679 chr21 48129895 1655421 0.03439485999294201 0.32725771325184444 chr22 51304566 3356518 0.06542337771651748 0.3162565573534335 chrMT 16571 19751 1.1919015146943455 1.4230856300787251 chrX 155270560 8332352 0.053663437550556914 0.34003961297353563 chrY 59373566 529351 0.008915600588989383 0.30984695234387255