BamQC report ----------------------------------- >>>>>>> Input bam file = SRR10524640.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 = 1,560,866 number of mapped reads = 912,659 (58.47%) number of supplementary alignments = 3,297 (0.21%) number of secondary alignments = 0 number of mapped bases = 52,799,373 bp number of sequenced bases = 52,782,082 bp number of aligned bases = 0 bp number of duplicated reads (estimated) = 35,960 duplication rate = 3.07% >>>>>>> Insert size mean insert size = 0 std insert size = 0 median insert size = 0 >>>>>>> Mapping quality mean mapping quality = 44.458 >>>>>>> ACTG content number of A's = 12,428,767 bp (23.55%) number of C's = 10,742,351 bp (20.35%) number of T's = 17,032,320 bp (32.27%) number of G's = 12,578,193 bp (23.83%) number of N's = 451 bp (0%) GC percentage = 44.18% >>>>>>> Mismatches and indels general error rate = 0.0053 number of mismatches = 272,828 number of insertions = 3,167 mapped reads with insertion percentage = 0.34% number of deletions = 10,316 mapped reads with deletion percentage = 1.12% homopolymer indels = 44.29% >>>>>>> Coverage mean coverageData = 0.0171X std coverageData = 0.1853X There is a 1.54% of reference with a coverageData >= 1X There is a 0.12% of reference with a coverageData >= 2X There is a 0.02% 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 5383327 0.021598048495935343 0.3211894950813231 chr2 243199373 4714960 0.01938722103531081 0.22651324385924806 chr3 198022430 3308218 0.016706279182615826 0.1395654908971427 chr4 191154276 2387091 0.01248777191884528 0.13993228296314295 chr5 180915260 3253691 0.01798461334881314 0.14494078814265146 chr6 171115067 3437716 0.020090083592697306 0.16108318660891005 chr7 159138663 3207730 0.020156823863726945 0.21485355955479127 chr8 146364022 4618867 0.03155739325064461 0.24655446462681252 chr9 141213431 1923865 0.013623810330052812 0.15002071417812302 chr10 135534747 2343045 0.017287411913640124 0.18892798472123393 chr11 135006516 2697548 0.019980872626918243 0.1724925851686594 chr12 133851895 1634658 0.01221243823257041 0.12251249891289193 chr13 115169878 1282641 0.011136948499676278 0.11571533949988588 chr14 107349540 970668 0.009042125378459935 0.10866441709573837 chr15 102531392 1388290 0.01354014583162979 0.12691211427424937 chr16 90354753 1589995 0.017597248038517685 0.14887829286591434 chr17 81195210 1212282 0.014930462030949856 0.13685677354953626 chr18 78077248 1387607 0.01777223244343858 0.22972979133330906 chr19 59128983 1078231 0.018235236685873662 0.21870577493003046 chr20 63025520 987202 0.0156635280438781 0.13745850123433664 chr21 48129895 471496 0.009796323054517364 0.12307171745244436 chr22 51304566 1010122 0.019688734916888294 0.15232803064568431 chrMT 16571 3867 0.23335948343491641 0.5122716430661898 chrX 155270560 2348759 0.015126879171428248 0.1412488605108329 chrY 59373566 157497 0.0026526451181995707 0.11209136002801673