BamQC report ----------------------------------- >>>>>>> Input bam file = SRR3472642.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 = 18,025,204 number of mapped reads = 17,889,072 (99.24%) number of supplementary alignments = 84,396 (0.47%) number of secondary alignments = 0 number of mapped paired reads (first in pair) = 8,973,551 number of mapped paired reads (second in pair) = 8,915,521 number of mapped paired reads (both in pair) = 17,793,936 number of mapped paired reads (singletons) = 95,136 number of mapped bases = 1,762,675,672 bp number of sequenced bases = 1,762,454,596 bp number of aligned bases = 0 bp number of duplicated reads (estimated) = 12,881,931 duplication rate = 49.04% >>>>>>> Insert size mean insert size = 19,607.2502 std insert size = 1,336,706.1228 median insert size = 213 >>>>>>> Mapping quality mean mapping quality = 54.7965 >>>>>>> ACTG content number of A's = 487,420,604 bp (27.66%) number of C's = 395,304,820 bp (22.43%) number of T's = 490,057,002 bp (27.81%) number of G's = 389,346,173 bp (22.09%) number of N's = 325,997 bp (0.02%) GC percentage = 44.52% >>>>>>> Mismatches and indels general error rate = 0.0059 number of mismatches = 10,274,098 number of insertions = 107,987 mapped reads with insertion percentage = 0.6% number of deletions = 95,927 mapped reads with deletion percentage = 0.53% homopolymer indels = 46.01% >>>>>>> Coverage mean coverageData = 0.5694X std coverageData = 33.9135X There is a 3.51% of reference with a coverageData >= 1X There is a 1.61% of reference with a coverageData >= 2X There is a 0.76% of reference with a coverageData >= 3X There is a 0.58% of reference with a coverageData >= 4X There is a 0.44% of reference with a coverageData >= 5X There is a 0.39% of reference with a coverageData >= 6X There is a 0.35% of reference with a coverageData >= 7X There is a 0.33% of reference with a coverageData >= 8X There is a 0.31% of reference with a coverageData >= 9X There is a 0.3% of reference with a coverageData >= 10X There is a 0.28% of reference with a coverageData >= 11X There is a 0.27% of reference with a coverageData >= 12X There is a 0.27% of reference with a coverageData >= 13X There is a 0.26% of reference with a coverageData >= 14X There is a 0.25% of reference with a coverageData >= 15X There is a 0.24% of reference with a coverageData >= 16X There is a 0.24% of reference with a coverageData >= 17X There is a 0.23% of reference with a coverageData >= 18X There is a 0.22% of reference with a coverageData >= 19X There is a 0.22% of reference with a coverageData >= 20X There is a 0.21% of reference with a coverageData >= 21X There is a 0.21% of reference with a coverageData >= 22X There is a 0.2% of reference with a coverageData >= 23X There is a 0.2% of reference with a coverageData >= 24X There is a 0.2% of reference with a coverageData >= 25X There is a 0.19% of reference with a coverageData >= 26X There is a 0.19% of reference with a coverageData >= 27X There is a 0.19% of reference with a coverageData >= 28X There is a 0.18% of reference with a coverageData >= 29X There is a 0.18% of reference with a coverageData >= 30X There is a 0.18% of reference with a coverageData >= 31X There is a 0.17% of reference with a coverageData >= 32X There is a 0.17% of reference with a coverageData >= 33X There is a 0.17% of reference with a coverageData >= 34X There is a 0.17% of reference with a coverageData >= 35X There is a 0.16% of reference with a coverageData >= 36X There is a 0.16% of reference with a coverageData >= 37X There is a 0.16% of reference with a coverageData >= 38X There is a 0.16% of reference with a coverageData >= 39X There is a 0.15% of reference with a coverageData >= 40X There is a 0.15% of reference with a coverageData >= 41X There is a 0.15% of reference with a coverageData >= 42X There is a 0.15% of reference with a coverageData >= 43X There is a 0.15% of reference with a coverageData >= 44X There is a 0.15% of reference with a coverageData >= 45X There is a 0.14% of reference with a coverageData >= 46X There is a 0.14% of reference with a coverageData >= 47X There is a 0.14% of reference with a coverageData >= 48X There is a 0.14% of reference with a coverageData >= 49X There is a 0.14% of reference with a coverageData >= 50X There is a 0.14% of reference with a coverageData >= 51X >>>>>>> Coverage per contig chr1 249250621 306283818 1.2288186756413337 57.50773073940629 chr2 243199373 193540006 0.7958079974161776 76.26705578458859 chr3 198022430 166881945 0.8427426377910826 35.114346861259165 chr4 191154276 49745259 0.2602361822133657 12.115661149836274 chr5 180915260 107499557 0.5941983943200811 30.757923177684102 chr6 171115067 105054799 0.613942423901222 21.22589677242994 chr7 159138663 60928907 0.38286677700691757 19.600941743201734 chr8 146364022 120147387 0.8208806054810383 35.274491472062536 chr9 141213431 52584252 0.3723742963231309 16.759963835772503 chr10 135534747 27859179 0.2055500867242553 8.642048718506343 chr11 135006516 44704962 0.33113188403439725 12.573712731738938 chr12 133851895 71325760 0.5328707524088471 22.505803127913083 chr13 115169878 36826941 0.31976191726103936 13.837251693354947 chr14 107349540 30210306 0.28141998559099557 13.305528393235221 chr15 102531392 38620271 0.376667772149236 15.831504138411491 chr16 90354753 84930237 0.9399642429435893 30.889919532980823 chr17 81195210 62782159 0.7732249106813074 23.56287003421867 chr18 78077248 28500573 0.36503045035603715 13.314783750004722 chr19 59128983 25057774 0.4237815827138444 11.076864423729596 chr20 63025520 37278897 0.5914889238517984 20.050296358606207 chr21 48129895 13182584 0.27389596424426027 16.915312454248333 chr22 51304566 15752009 0.3070293782428644 11.91904360522615 chrMT 16571 1792 0.10814072777744252 0.4472143927046979 chrX 155270560 81521544 0.5250289816691587 31.388641367521185 chrY 59373566 1454754 0.024501711755025798 1.1318063910802898