BamQC report ----------------------------------- >>>>>>> Input bam file = SRR1039846.sorted.bam outfile = /home/luna/rawdata/yangyxdownload/SRP030642/SRP030642.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 = 10,030,984 number of mapped reads = 8,600,919 (85.74%) number of secondary alignments = 0 number of mapped paired reads (first in pair) = 4,364,057 number of mapped paired reads (second in pair) = 4,236,862 number of mapped paired reads (both in pair) = 7,726,638 number of mapped paired reads (singletons) = 874,281 number of mapped bases = 331,112,188 bp number of sequenced bases = 331,078,584 bp number of aligned bases = 0 bp number of duplicated reads (estimated) = 1,187,795 duplication rate = 12.35% >>>>>>> Insert size mean insert size = 87,296.8709 std insert size = 2,872,518.24 median insert size = 92 >>>>>>> Mapping quality mean mapping quality = 45.4643 >>>>>>> ACTG content number of A's = 85,708,800 bp (25.89%) number of C's = 75,418,220 bp (22.78%) number of T's = 89,199,724 bp (26.94%) number of G's = 80,738,820 bp (24.39%) number of N's = 13,020 bp (0%) GC percentage = 47.17% >>>>>>> Mismatches and indels general error rate = 0.0055 number of mismatches = 1,804,884 number of insertions = 11,164 mapped reads with insertion percentage = 0.13% number of deletions = 26,728 mapped reads with deletion percentage = 0.31% homopolymer indels = 43.65% >>>>>>> Coverage mean coverageData = 0.107X std coverageData = 0.7432X There is a 4.05% of reference with a coverageData >= 1X There is a 2.33% of reference with a coverageData >= 2X There is a 1.47% of reference with a coverageData >= 3X There is a 0.96% of reference with a coverageData >= 4X There is a 0.63% of reference with a coverageData >= 5X There is a 0.41% of reference with a coverageData >= 6X There is a 0.27% of reference with a coverageData >= 7X There is a 0.18% of reference with a coverageData >= 8X There is a 0.12% of reference with a coverageData >= 9X There is a 0.08% of reference with a coverageData >= 10X There is a 0.05% of reference with a coverageData >= 11X There is a 0.04% of reference with a coverageData >= 12X There is a 0.02% of reference with a coverageData >= 13X There is a 0.02% of reference with a coverageData >= 14X There is a 0.01% of reference with a coverageData >= 15X There is a 0.01% of reference with a coverageData >= 16X There is a 0.01% of reference with a coverageData >= 17X There is a 0.01% 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 28448771 0.11413721211952367 0.8238705104929093 chr2 243199373 28492776 0.11715809810085324 0.7947241303380945 chr3 198022430 22038710 0.1112940084615667 0.7038913250820309 chr4 191154276 20192679 0.10563550772989248 0.6997541880680294 chr5 180915260 19523303 0.10791407535218422 0.6938791959407328 chr6 171115067 18673955 0.10913098026604519 0.7617920352773796 chr7 159138663 17837548 0.11208808509343829 0.7902514561406593 chr8 146364022 16151548 0.11035190055107942 0.7912562078951783 chr9 141213431 13789361 0.09764907560386377 0.6663382263866455 chr10 135534747 16273184 0.12006650958665234 0.7661645664032356 chr11 135006516 15637337 0.1158265353651523 0.8971214620583374 chr12 133851895 15196225 0.11353014464233024 0.7167534838188574 chr13 115169878 9981545 0.08666801748283523 0.6275821269075056 chr14 107349540 10540979 0.09819305234097883 0.6754825391528594 chr15 102531392 10362841 0.10106993378184118 0.6880442299513949 chr16 90354753 10771709 0.11921574286191673 0.781961957495199 chr17 81195210 10611673 0.13069333769812283 0.8110398116449603 chr18 78077248 8199686 0.10502017181753127 0.7437386528939094 chr19 59128983 8239585 0.13934934412790426 0.9868456569825168 chr20 63025520 7940854 0.12599426391087293 0.780996012259546 chr21 48129895 4261258 0.08853661534063184 0.6671064457333334 chr22 51304566 5624556 0.10963071006194654 0.7574018336105546 chrMT 16571 84823 5.118761692112727 8.730655754078152 chrX 155270560 10079853 0.06491799218087446 0.5310875684848317 chrY 59373566 2157429 0.03633652390021512 0.4192617983575581