BamQC report ----------------------------------- >>>>>>> Input bam file = SRR617378.sorted.bam outfile = /home/luna/rawdata/yangyxdownload/SRP017032/SRP017032.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 = 32,000,000 number of mapped reads = 29,758,023 (92.99%) number of supplementary alignments = 65,216 (0.2%) number of secondary alignments = 0 number of mapped paired reads (first in pair) = 14,949,052 number of mapped paired reads (second in pair) = 14,808,971 number of mapped paired reads (both in pair) = 29,180,752 number of mapped paired reads (singletons) = 577,271 number of mapped bases = 2,917,624,321 bp number of sequenced bases = 2,916,783,966 bp number of aligned bases = 0 bp number of duplicated reads (estimated) = 1,527,546 duplication rate = 1.47% >>>>>>> Insert size mean insert size = 50,344.7424 std insert size = 2,134,503.6971 median insert size = 209 >>>>>>> Mapping quality mean mapping quality = 53.4234 >>>>>>> ACTG content number of A's = 886,018,105 bp (30.38%) number of C's = 577,416,007 bp (19.8%) number of T's = 872,062,368 bp (29.9%) number of G's = 579,881,676 bp (19.88%) number of N's = 1,405,810 bp (0.05%) GC percentage = 39.68% >>>>>>> Mismatches and indels general error rate = 0.0128 number of mismatches = 36,508,727 number of insertions = 289,708 mapped reads with insertion percentage = 0.94% number of deletions = 350,095 mapped reads with deletion percentage = 1.14% homopolymer indels = 41.05% >>>>>>> Coverage mean coverageData = 0.9425X std coverageData = 9.6363X There is a 52.37% of reference with a coverageData >= 1X There is a 23.52% of reference with a coverageData >= 2X There is a 9.02% of reference with a coverageData >= 3X There is a 3.17% of reference with a coverageData >= 4X There is a 1.09% of reference with a coverageData >= 5X There is a 0.4% of reference with a coverageData >= 6X There is a 0.18% of reference with a coverageData >= 7X There is a 0.1% of reference with a coverageData >= 8X There is a 0.07% of reference with a coverageData >= 9X There is a 0.06% 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 0.04% of reference with a coverageData >= 13X There is a 0.03% of reference with a coverageData >= 14X There is a 0.03% of reference with a coverageData >= 15X There is a 0.03% of reference with a coverageData >= 16X There is a 0.03% of reference with a coverageData >= 17X There is a 0.03% of reference with a coverageData >= 18X There is a 0.03% of reference with a coverageData >= 19X There is a 0.02% of reference with a coverageData >= 20X There is a 0.02% of reference with a coverageData >= 21X There is a 0.02% of reference with a coverageData >= 22X There is a 0.02% of reference with a coverageData >= 23X There is a 0.02% of reference with a coverageData >= 24X There is a 0.02% of reference with a coverageData >= 25X There is a 0.02% of reference with a coverageData >= 26X There is a 0.02% of reference with a coverageData >= 27X There is a 0.02% of reference with a coverageData >= 28X There is a 0.02% of reference with a coverageData >= 29X There is a 0.02% of reference with a coverageData >= 30X There is a 0.02% of reference with a coverageData >= 31X There is a 0.02% of reference with a coverageData >= 32X There is a 0.02% of reference with a coverageData >= 33X There is a 0.02% of reference with a coverageData >= 34X There is a 0.02% of reference with a coverageData >= 35X There is a 0.02% of reference with a coverageData >= 36X There is a 0.01% of reference with a coverageData >= 37X There is a 0.01% of reference with a coverageData >= 38X There is a 0.01% of reference with a coverageData >= 39X There is a 0.01% of reference with a coverageData >= 40X There is a 0.01% of reference with a coverageData >= 41X There is a 0.01% of reference with a coverageData >= 42X There is a 0.01% of reference with a coverageData >= 43X There is a 0.01% of reference with a coverageData >= 44X There is a 0.01% of reference with a coverageData >= 45X There is a 0.01% of reference with a coverageData >= 46X There is a 0.01% of reference with a coverageData >= 47X There is a 0.01% of reference with a coverageData >= 48X There is a 0.01% of reference with a coverageData >= 49X There is a 0.01% of reference with a coverageData >= 50X There is a 0.01% of reference with a coverageData >= 51X >>>>>>> Coverage per contig chr1 249250621 189108879 0.7587097606468952 19.67264755254317 chr2 243199373 288130793 1.184751380917417 8.571386367927309 chr3 198022430 232766617 1.1754558157881407 1.4783663059828278 chr4 191154276 160570594 0.8400052426763396 8.971838801069792 chr5 180915260 183891382 1.0164503646624392 1.4530714845327253 chr6 171115067 136949330 0.8003347244693537 3.658314027321622 chr7 159138663 236760016 1.4877592379923412 10.839081247840141 chr8 146364022 123136479 0.8413029193745442 7.332411157519247 chr9 141213431 122976148 0.8708530564631632 14.665407975708904 chr10 135534747 122955284 0.907186435372178 19.95161221881805 chr11 135006516 156634322 1.1601982381354097 5.491769712945064 chr12 133851895 128852632 0.9626507865279008 1.353030284904507 chr13 115169878 127799127 1.1096575703588052 1.2898021652524747 chr14 107349540 84069234 0.7831354843253171 1.3509605739384356 chr15 102531392 65315501 0.637029301230983 0.9672329761007723 chr16 90354753 72899351 0.8068125757590195 7.963908704109955 chr17 81195210 89953824 1.1078710677637265 7.05292369926378 chr18 78077248 52705748 0.675046179906341 15.017186633109212 chr19 59128983 53279339 0.901069768103402 9.350798741799169 chr20 63025520 83061450 1.3179018594372565 2.362390122158826 chr21 48129895 46616920 0.9685647558549629 3.1767560305268847 chr22 51304566 25567429 0.498346073135089 0.8969144065267467 chrMT 16571 1946012 117.43479572747572 21.15915260203125 chrX 155270560 121887430 0.7850002601909853 2.9362368989759524 chrY 59373566 9790480 0.16489627724230005 7.974075236097531