BamQC report ----------------------------------- >>>>>>> Input bam file = SRR3472529.sorted.bam outfile = /home/luna/rawdata/yangyxdownload/SRP074289/SRP074289.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 = 6,543,836 number of mapped reads = 6,450,875 (98.58%) number of supplementary alignments = 25,559 (0.39%) number of secondary alignments = 0 number of mapped paired reads (first in pair) = 3,236,372 number of mapped paired reads (second in pair) = 3,214,503 number of mapped paired reads (both in pair) = 6,405,904 number of mapped paired reads (singletons) = 44,971 number of mapped bases = 634,338,440 bp number of sequenced bases = 634,260,440 bp number of aligned bases = 0 bp number of duplicated reads (estimated) = 3,331,003 duplication rate = 41.41% >>>>>>> Insert size mean insert size = 28,735.2613 std insert size = 1,661,549.0983 median insert size = 222 >>>>>>> Mapping quality mean mapping quality = 55.0931 >>>>>>> ACTG content number of A's = 172,558,131 bp (27.21%) number of C's = 145,600,133 bp (22.96%) number of T's = 171,547,889 bp (27.05%) number of G's = 144,453,731 bp (22.78%) number of N's = 100,556 bp (0.02%) GC percentage = 45.73% >>>>>>> Mismatches and indels general error rate = 0.0059 number of mismatches = 3,646,030 number of insertions = 33,023 mapped reads with insertion percentage = 0.51% number of deletions = 32,400 mapped reads with deletion percentage = 0.5% homopolymer indels = 42.49% >>>>>>> Coverage mean coverageData = 0.2049X std coverageData = 7.4869X There is a 2.29% of reference with a coverageData >= 1X There is a 1.05% of reference with a coverageData >= 2X There is a 0.51% of reference with a coverageData >= 3X There is a 0.4% of reference with a coverageData >= 4X There is a 0.32% of reference with a coverageData >= 5X There is a 0.29% of reference with a coverageData >= 6X There is a 0.27% of reference with a coverageData >= 7X There is a 0.25% of reference with a coverageData >= 8X There is a 0.24% of reference with a coverageData >= 9X There is a 0.22% of reference with a coverageData >= 10X There is a 0.21% of reference with a coverageData >= 11X There is a 0.2% of reference with a coverageData >= 12X There is a 0.2% of reference with a coverageData >= 13X There is a 0.19% of reference with a coverageData >= 14X There is a 0.18% of reference with a coverageData >= 15X There is a 0.17% of reference with a coverageData >= 16X There is a 0.17% of reference with a coverageData >= 17X There is a 0.16% of reference with a coverageData >= 18X There is a 0.16% of reference with a coverageData >= 19X There is a 0.15% of reference with a coverageData >= 20X There is a 0.15% of reference with a coverageData >= 21X There is a 0.14% of reference with a coverageData >= 22X There is a 0.14% of reference with a coverageData >= 23X There is a 0.14% of reference with a coverageData >= 24X There is a 0.13% of reference with a coverageData >= 25X There is a 0.13% of reference with a coverageData >= 26X There is a 0.13% of reference with a coverageData >= 27X There is a 0.12% of reference with a coverageData >= 28X There is a 0.12% of reference with a coverageData >= 29X There is a 0.12% of reference with a coverageData >= 30X There is a 0.11% of reference with a coverageData >= 31X There is a 0.11% of reference with a coverageData >= 32X There is a 0.11% of reference with a coverageData >= 33X There is a 0.11% of reference with a coverageData >= 34X There is a 0.1% of reference with a coverageData >= 35X There is a 0.1% of reference with a coverageData >= 36X There is a 0.1% of reference with a coverageData >= 37X There is a 0.1% of reference with a coverageData >= 38X There is a 0.1% of reference with a coverageData >= 39X There is a 0.09% of reference with a coverageData >= 40X There is a 0.09% of reference with a coverageData >= 41X There is a 0.09% of reference with a coverageData >= 42X There is a 0.09% of reference with a coverageData >= 43X There is a 0.09% of reference with a coverageData >= 44X There is a 0.09% of reference with a coverageData >= 45X There is a 0.09% of reference with a coverageData >= 46X There is a 0.08% of reference with a coverageData >= 47X There is a 0.08% of reference with a coverageData >= 48X There is a 0.08% of reference with a coverageData >= 49X There is a 0.08% of reference with a coverageData >= 50X There is a 0.08% of reference with a coverageData >= 51X >>>>>>> Coverage per contig chr1 249250621 78893921 0.3165244711667138 11.92715240491263 chr2 243199373 40647784 0.16713770063872657 5.960091278013087 chr3 198022430 58952065 0.29770397727166564 7.932424804189177 chr4 191154276 23522859 0.12305693334320181 4.938718241448662 chr5 180915260 33181422 0.18340864115055855 6.063772552099015 chr6 171115067 50629153 0.29587782004024227 9.99016467621961 chr7 159138663 22494136 0.14134928354902668 4.174158102320271 chr8 146364022 24469401 0.16718180236943747 5.4655095634256385 chr9 141213431 36679853 0.25974762273143837 7.347540056044554 chr10 135534747 18751203 0.13834978420699748 5.705810151886913 chr11 135006516 40388957 0.29916301965751046 11.267161867996242 chr12 133851895 35490312 0.2651461303554948 8.286386128763318 chr13 115169878 16610597 0.14422692190400688 7.119749141311921 chr14 107349540 13409687 0.12491611049288148 5.447609178573291 chr15 102531392 14407854 0.14052139270673317 4.228140958758626 chr16 90354753 20263804 0.22426937518162438 8.190646049164108 chr17 81195210 31555290 0.3886348714413079 10.916525722513803 chr18 78077248 10298133 0.13189672105246333 4.989782495561449 chr19 59128983 10412227 0.17609345657103556 4.508864620955557 chr20 63025520 12308897 0.19530020537712342 8.845431250762324 chr21 48129895 1841425 0.03825948508717918 1.179092596158692 chr22 51304566 7496750 0.1461224718283359 5.3037045652690376 chrMT 16571 873 0.05268239695854203 0.2633220443330825 chrX 155270560 29494606 0.18995620290156742 6.500398796388811 chrY 59373566 2137231 0.03599633884210357 2.255973029742618