BamQC report ----------------------------------- >>>>>>> Input bam file = SRR3080738.sorted.bam outfile = /home/luna/rawdata/yangyxdownload/SRP064210/SRP064210.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 = 6,077,611 number of mapped reads = 4,260,935 (70.11%) number of supplementary alignments = 31,761 (0.52%) number of secondary alignments = 0 number of mapped bases = 271,846,530 bp number of sequenced bases = 271,752,049 bp number of aligned bases = 0 bp number of duplicated reads (estimated) = 593,641 duplication rate = 11.13% >>>>>>> Insert size mean insert size = 0 std insert size = 0 median insert size = 0 >>>>>>> Mapping quality mean mapping quality = 45.0085 >>>>>>> ACTG content number of A's = 82,100,450 bp (30.21%) number of C's = 54,876,255 bp (20.19%) number of T's = 74,481,043 bp (27.41%) number of G's = 60,209,733 bp (22.16%) number of N's = 84,568 bp (0.03%) GC percentage = 42.35% >>>>>>> Mismatches and indels general error rate = 0.0091 number of mismatches = 2,428,988 number of insertions = 20,290 mapped reads with insertion percentage = 0.47% number of deletions = 51,712 mapped reads with deletion percentage = 1.2% homopolymer indels = 43.38% >>>>>>> Coverage mean coverageData = 0.0878X std coverageData = 0.6285X There is a 5.6% of reference with a coverageData >= 1X There is a 1.76% of reference with a coverageData >= 2X There is a 0.69% of reference with a coverageData >= 3X There is a 0.3% of reference with a coverageData >= 4X There is a 0.14% of reference with a coverageData >= 5X There is a 0.07% of reference with a coverageData >= 6X There is a 0.04% of reference with a coverageData >= 7X There is a 0.02% of reference with a coverageData >= 8X There is a 0.02% of reference with a coverageData >= 9X There is a 0.01% of reference with a coverageData >= 10X There is a 0.01% of reference with a coverageData >= 11X There is a 0.01% 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 21799292 0.08745932873723913 0.7306159474806794 chr2 243199373 22911133 0.0942072042266326 0.6477558875410574 chr3 198022430 18169830 0.09175642375462215 0.45355339944362266 chr4 191154276 17685613 0.09252010140751442 0.5077333119080354 chr5 180915260 16470688 0.09104089947967905 0.45337390050492554 chr6 171115067 15675541 0.09160818667125321 0.8114083826143381 chr7 159138663 14880864 0.09350879113518756 0.884673431202638 chr8 146364022 13886963 0.09487962144139493 0.967675509587773 chr9 141213431 10973917 0.07771156696844225 0.5347170299070779 chr10 135534747 13189845 0.09731707397513348 0.6573840726838289 chr11 135006516 12301156 0.09111527624340739 0.6654185316162181 chr12 133851895 12145585 0.09073898430799206 0.4576404566823176 chr13 115169878 8824755 0.07662381130593887 0.4093213402900381 chr14 107349540 8495409 0.07913782397204497 0.4804085667608551 chr15 102531392 7834811 0.07641377774330811 0.41637350502195475 chr16 90354753 7745625 0.0857245993467549 0.4814380180437348 chr17 81195210 7093346 0.08736163130805376 0.4618442507803243 chr18 78077248 7294985 0.09343291659050278 0.9886022176647141 chr19 59128983 5486484 0.09278840463060221 0.7891854885575332 chr20 63025520 5901589 0.09363808501698995 0.47590881578560307 chr21 48129895 3584317 0.07447173944593065 0.46463608598737594 chr22 51304566 3037458 0.059204438061126956 0.3655241687151746 chrMT 16571 71629 4.322551445295999 4.390992665883377 chrX 155270560 15533753 0.10004313116407901 0.5240410768145695 chrY 59373566 851942 0.014348843389329183 0.4307337273625172