BamQC report ----------------------------------- >>>>>>> Input bam file = SRR6068096.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 = 1,011,262 number of mapped reads = 852,362 (84.29%) number of supplementary alignments = 6,233 (0.62%) number of secondary alignments = 0 number of mapped bases = 57,792,049 bp number of sequenced bases = 57,764,366 bp number of aligned bases = 0 bp number of duplicated reads (estimated) = 19,237 duplication rate = 1.64% >>>>>>> Insert size mean insert size = 0 std insert size = 0 median insert size = 0 >>>>>>> Mapping quality mean mapping quality = 44.9475 >>>>>>> ACTG content number of A's = 17,147,286 bp (29.68%) number of C's = 10,449,540 bp (18.09%) number of T's = 17,688,801 bp (30.62%) number of G's = 12,477,598 bp (21.6%) number of N's = 1,141 bp (0%) GC percentage = 39.69% >>>>>>> Mismatches and indels general error rate = 0.0105 number of mismatches = 597,521 number of insertions = 4,866 mapped reads with insertion percentage = 0.57% number of deletions = 16,799 mapped reads with deletion percentage = 1.95% homopolymer indels = 45.41% >>>>>>> Coverage mean coverageData = 0.0187X std coverageData = 0.2285X There is a 1.73% of reference with a coverageData >= 1X There is a 0.1% of reference with a coverageData >= 2X There is a 0.01% 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 7041023 0.028248768134463344 0.5105871721632496 chr2 243199373 4886213 0.020091388146794276 0.2030282877817227 chr3 198022430 4559337 0.023024346282388312 0.1596700617322789 chr4 191154276 3774364 0.019745119382001165 0.1484731319370283 chr5 180915260 3244550 0.017934086931085856 0.1404413576741678 chr6 171115067 4665883 0.027267517009475266 0.20124130339411497 chr7 159138663 5139510 0.032295797282147584 0.22449443600154417 chr8 146364022 2739217 0.01871509789475449 0.3569074503543144 chr9 141213431 1533428 0.01085893876482613 0.15312833967857756 chr10 135534747 2310831 0.017049731165986536 0.19739308016856102 chr11 135006516 2878289 0.021319630231773405 0.17866683843018213 chr12 133851895 1935298 0.01445850281013952 0.130284922286911 chr13 115169878 1006270 0.008737267221903282 0.09782533703268048 chr14 107349540 1396956 0.013013153107130221 0.1256968048160555 chr15 102531392 902717 0.008804298687371766 0.09915501640728448 chr16 90354753 1644284 0.018198090807685568 0.15148202963485052 chr17 81195210 1550781 0.01909941485464475 0.15329797098673367 chr18 78077248 1759698 0.022537910147652745 0.27541269647381056 chr19 59128983 927852 0.015691999979096545 0.32584915562243666 chr20 63025520 697225 0.011062582268262126 0.11775517832231713 chr21 48129895 786544 0.01634210920260682 0.13666642609439472 chr22 51304566 474601 0.009250658118811492 0.10092038447782369 chrMT 16571 15499 0.9353086717759942 1.1606744609428201 chrX 155270560 1812001 0.011669958554925029 0.124328838965771 chrY 59373566 109678 0.0018472530351301452 0.05019143786028116