BamQC report ----------------------------------- >>>>>>> Input bam file = SRR3084901.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 = 2,405,015 number of mapped reads = 2,199,194 (91.44%) number of supplementary alignments = 14,178 (0.59%) number of secondary alignments = 0 number of mapped bases = 150,605,038 bp number of sequenced bases = 150,547,426 bp number of aligned bases = 0 bp number of duplicated reads (estimated) = 101,749 duplication rate = 3.98% >>>>>>> Insert size mean insert size = 0 std insert size = 0 median insert size = 0 >>>>>>> Mapping quality mean mapping quality = 47.1391 >>>>>>> ACTG content number of A's = 42,971,863 bp (28.54%) number of C's = 27,605,771 bp (18.34%) number of T's = 48,070,699 bp (31.93%) number of G's = 31,875,226 bp (21.17%) number of N's = 23,867 bp (0.02%) GC percentage = 39.51% >>>>>>> Mismatches and indels general error rate = 0.0082 number of mismatches = 1,217,223 number of insertions = 11,368 mapped reads with insertion percentage = 0.51% number of deletions = 33,279 mapped reads with deletion percentage = 1.5% homopolymer indels = 48.51% >>>>>>> Coverage mean coverageData = 0.0486X std coverageData = 0.3535X There is a 4.16% of reference with a coverageData >= 1X There is a 0.55% of reference with a coverageData >= 2X There is a 0.08% of reference with a coverageData >= 3X There is a 0.02% 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 13112955 0.05260951787157232 0.6292481124898276 chr2 243199373 12871461 0.05292555174474072 0.4254035999662816 chr3 198022430 12967463 0.06548481906822373 0.28949485052200713 chr4 191154276 6479145 0.03389484732217029 0.2097702024750011 chr5 180915260 7887502 0.04359777058054694 0.23909941704142632 chr6 171115067 9496782 0.0554993909449248 0.2729235869576412 chr7 159138663 8123454 0.051046388394000775 0.38463529189607504 chr8 146364022 7559183 0.05164645584828217 0.455683131035493 chr9 141213431 11581105 0.08201135627106178 0.4355376849382389 chr10 135534747 4883573 0.036031889298468976 0.286755784305685 chr11 135006516 8019187 0.05939851821670593 0.33092536442195114 chr12 133851895 6215295 0.04643412033875202 0.2501794628466541 chr13 115169878 3457550 0.030021304702606354 0.19349803012025363 chr14 107349540 2982329 0.027781479082257827 0.19574549502946095 chr15 102531392 3778352 0.036850684715174845 0.21519026771559474 chr16 90354753 3141493 0.03476843105309579 0.23048526785821571 chr17 81195210 4398152 0.05416762885396811 0.2716244175922444 chr18 78077248 5812232 0.07444207049920612 0.5619623859420908 chr19 59128983 2681297 0.04534657732909088 0.4108954529393652 chr20 63025520 3115257 0.049428501343582724 0.25137718461218506 chr21 48129895 1347632 0.0279998948678363 0.19891801865783904 chr22 51304566 1537099 0.02996027682994141 0.19292709612314607 chrMT 16571 24820 1.497797356828194 1.481335629320078 chrX 155270560 8861108 0.05706882231892511 0.2897043519338785 chrY 59373566 270612 0.004557785867198881 0.11324784725995203