BamQC report ----------------------------------- >>>>>>> Input bam file = SRR6236091.sorted.bam outfile = /home/luna/rawdata/yangyxdownload/SRP116771/SRP116771.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 = 2,170,457 number of mapped reads = 1,880,933 (86.66%) number of supplementary alignments = 9,262 (0.43%) number of secondary alignments = 0 number of mapped bases = 122,020,253 bp number of sequenced bases = 121,961,339 bp number of aligned bases = 0 bp number of duplicated reads (estimated) = 86,242 duplication rate = 3.57% >>>>>>> Insert size mean insert size = 0 std insert size = 0 median insert size = 0 >>>>>>> Mapping quality mean mapping quality = 44.6451 >>>>>>> ACTG content number of A's = 32,595,378 bp (26.73%) number of C's = 21,949,884 bp (18%) number of T's = 38,883,816 bp (31.88%) number of G's = 28,470,449 bp (23.34%) number of N's = 61,812 bp (0.05%) GC percentage = 41.34% >>>>>>> Mismatches and indels general error rate = 0.0084 number of mismatches = 1,004,701 number of insertions = 8,559 mapped reads with insertion percentage = 0.45% number of deletions = 33,984 mapped reads with deletion percentage = 1.79% homopolymer indels = 46.38% >>>>>>> Coverage mean coverageData = 0.0394X std coverageData = 0.3671X There is a 3.41% of reference with a coverageData >= 1X There is a 0.39% of reference with a coverageData >= 2X There is a 0.06% 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 10708987 0.042964735482043194 0.6322679340549376 chr2 243199373 7006404 0.02880930124766399 0.4139426276675445 chr3 198022430 8976039 0.04532839537420079 0.2389476915961486 chr4 191154276 6491758 0.033960830674800074 0.2251760243901124 chr5 180915260 7304604 0.04037583120406758 0.22702310719139046 chr6 171115067 11097293 0.06485281041908483 0.3831833027946701 chr7 159138663 8918381 0.056041573002281665 0.6310077708457011 chr8 146364022 8113279 0.05543219494200562 0.4711204418108447 chr9 141213431 5383622 0.03812400819012747 0.34596237746772146 chr10 135534747 4751267 0.035055711580735824 0.32033738863174255 chr11 135006516 3776038 0.027969301866881742 0.24804248413070626 chr12 133851895 5140174 0.0384019516496199 0.22752979214432126 chr13 115169878 5446590 0.04729179273768094 0.24478437584533563 chr14 107349540 2596330 0.024185758038646463 0.18953618451754695 chr15 102531392 3398448 0.03314543900857213 0.2154323029748426 chr16 90354753 3787263 0.041915481745603354 0.2526081134805268 chr17 81195210 2834767 0.0349129831673568 0.2323005738676033 chr18 78077248 3018950 0.03866619376748525 0.5295738871379346 chr19 59128983 2058686 0.034816868066207055 0.45523352599103606 chr20 63025520 2332126 0.03700288391115218 0.22101204005393577 chr21 48129895 1599474 0.03323244316240457 0.22833151752231368 chr22 51304566 1131611 0.022056730779088943 0.16366940732408305 chrMT 16571 121363 7.323818719449641 4.859561824955565 chrX 155270560 5759802 0.037095261329642915 0.24241522539011554 chrY 59373566 266997 0.004496900186187234 0.12157107791000894