BamQC report ----------------------------------- >>>>>>> Input bam file = SRR3124870.sorted.bam outfile = /home/luna/rawdata/yangyxdownload/SRP068920/SRP068920.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 = 4,743,698 number of mapped reads = 4,674,419 (98.54%) number of supplementary alignments = 14,317 (0.3%) number of secondary alignments = 0 number of mapped paired reads (first in pair) = 2,340,685 number of mapped paired reads (second in pair) = 2,333,734 number of mapped paired reads (both in pair) = 4,660,580 number of mapped paired reads (singletons) = 13,839 number of mapped bases = 407,833,956 bp number of sequenced bases = 407,634,873 bp number of aligned bases = 0 bp number of duplicated reads (estimated) = 329,092 duplication rate = 5.23% >>>>>>> Insert size mean insert size = 23,422.8557 std insert size = 1,399,980.9999 median insert size = 196 >>>>>>> Mapping quality mean mapping quality = 53.1181 >>>>>>> ACTG content number of A's = 114,419,290 bp (28.07%) number of C's = 76,564,685 bp (18.78%) number of T's = 120,635,199 bp (29.59%) number of G's = 96,010,556 bp (23.55%) number of N's = 5,143 bp (0%) GC percentage = 42.34% >>>>>>> Mismatches and indels general error rate = 0.0071 number of mismatches = 2,806,411 number of insertions = 50,522 mapped reads with insertion percentage = 1.06% number of deletions = 122,800 mapped reads with deletion percentage = 2.58% homopolymer indels = 48.91% >>>>>>> Coverage mean coverageData = 0.1317X std coverageData = 1.0573X There is a 9.31% of reference with a coverageData >= 1X There is a 2.41% of reference with a coverageData >= 2X There is a 0.66% of reference with a coverageData >= 3X There is a 0.24% of reference with a coverageData >= 4X There is a 0.1% of reference with a coverageData >= 5X There is a 0.05% of reference with a coverageData >= 6X There is a 0.03% of reference with a coverageData >= 7X There is a 0.02% of reference with a coverageData >= 8X There is a 0.01% 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 0.01% of reference with a coverageData >= 13X There is a 0.01% 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 35985997 0.14437675964707025 1.4662197200405693 chr2 243199373 30554285 0.12563471946122165 1.015657749258295 chr3 198022430 26952674 0.13610919732678767 0.4707116896044288 chr4 191154276 21694849 0.11349392466637785 0.6756052122787305 chr5 180915260 23835221 0.13174798521694633 0.46889977074656847 chr6 171115067 18924394 0.11059455097545559 0.6797143339146774 chr7 159138663 35303604 0.22184177832385082 1.8780834596127045 chr8 146364022 31565811 0.2156664634427715 0.8245054745047706 chr9 141213431 18595615 0.13168446420652438 1.2385544574520142 chr10 135534747 17979026 0.1326525219396322 2.237328906867094 chr11 135006516 19336144 0.14322378336168604 0.8010946347429589 chr12 133851895 20141948 0.15047936377740487 0.5019942835893758 chr13 115169878 12562537 0.10907832167713158 0.4187055304977069 chr14 107349540 10702886 0.09970127491929635 0.43088267506099864 chr15 102531392 8173319 0.07971528368599541 0.3608248363183694 chr16 90354753 13386089 0.14815035795626602 1.1331627832394087 chr17 81195210 11587739 0.14271456407342256 1.8676426845908267 chr18 78077248 7444540 0.09534839137772888 1.2385657072281138 chr19 59128983 5444556 0.09207931075019504 0.9008059384954374 chr20 63025520 7871891 0.12490005635812287 0.4676299619661415 chr21 48129895 3367928 0.06997580194180769 0.42422662251052196 chr22 51304566 3520085 0.06861153449772872 0.33707272019479 chrMT 16571 134991 8.146219298774968 6.029305702680548 chrX 155270560 19950693 0.12848986311378022 0.5987753562428664 chrY 59373566 2817134 0.04744761330319961 0.7956296048587649