BamQC report ----------------------------------- >>>>>>> Input bam file = SRR3124981.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 = 5,165,618 number of mapped reads = 4,947,923 (95.79%) number of supplementary alignments = 19,402 (0.38%) number of secondary alignments = 0 number of mapped paired reads (first in pair) = 2,516,608 number of mapped paired reads (second in pair) = 2,431,315 number of mapped paired reads (both in pair) = 4,833,888 number of mapped paired reads (singletons) = 114,035 number of mapped bases = 301,511,119 bp number of sequenced bases = 301,381,721 bp number of aligned bases = 0 bp number of duplicated reads (estimated) = 371,612 duplication rate = 4.34% >>>>>>> Insert size mean insert size = 90,181.0278 std insert size = 2,833,861.5095 median insert size = 167 >>>>>>> Mapping quality mean mapping quality = 51.19 >>>>>>> ACTG content number of A's = 84,303,499 bp (27.97%) number of C's = 52,571,780 bp (17.44%) number of T's = 92,612,712 bp (30.73%) number of G's = 71,893,730 bp (23.85%) number of N's = 0 bp (0%) GC percentage = 41.3% >>>>>>> Mismatches and indels general error rate = 0.0077 number of mismatches = 2,249,027 number of insertions = 35,537 mapped reads with insertion percentage = 0.71% number of deletions = 79,449 mapped reads with deletion percentage = 1.59% homopolymer indels = 46.11% >>>>>>> Coverage mean coverageData = 0.0974X std coverageData = 1.3126X There is a 7.55% of reference with a coverageData >= 1X There is a 1.27% of reference with a coverageData >= 2X There is a 0.26% of reference with a coverageData >= 3X There is a 0.08% of reference with a coverageData >= 4X There is a 0.04% of reference with a coverageData >= 5X There is a 0.02% of reference with a coverageData >= 6X There is a 0.02% of reference with a coverageData >= 7X There is a 0.01% 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 0.01% of reference with a coverageData >= 19X There is a 0.01% of reference with a coverageData >= 20X There is a 0.01% of reference with a coverageData >= 21X There is a 0.01% of reference with a coverageData >= 22X There is a 0.01% of reference with a coverageData >= 23X There is a 0.01% of reference with a coverageData >= 24X There is a 0.01% 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 24255632 0.09731422895833026 0.9151315457475502 chr2 243199373 27113143 0.11148525041633228 1.3357327247722877 chr3 198022430 20539539 0.10372329538628527 0.4643086828126881 chr4 191154276 20246028 0.10591459643832399 0.739832865224829 chr5 180915260 18624928 0.10294835272602211 0.41480972072769634 chr6 171115067 18471768 0.10794939524524745 0.6191056710930191 chr7 159138663 16954682 0.10654030692717331 0.9809871627046954 chr8 146364022 15629966 0.10678830621366772 0.4822243834315808 chr9 141213431 12148142 0.08602681709503963 0.8640228485752356 chr10 135534747 17170281 0.12668545432117123 4.826065603173275 chr11 135006516 13514429 0.10010204988920683 0.6082940085241888 chr12 133851895 13530967 0.10108909552606633 0.3893391079662512 chr13 115169878 9390871 0.08153929797511811 0.33525778333431633 chr14 107349540 9069032 0.08448133080029965 0.439327211309404 chr15 102531392 8388517 0.08181413356799057 0.3730181320152494 chr16 90354753 10431358 0.1154489127982011 2.168393411468472 chr17 81195210 6604741 0.08134397336985766 0.7515178604945857 chr18 78077248 8047324 0.10306874545578246 1.2996143617729787 chr19 59128983 3996751 0.06759377207620838 0.7672787566805236 chr20 63025520 6004155 0.09526545754799008 0.5920404096668074 chr21 48129895 3864223 0.08028737648399191 0.4876314710107363 chr22 51304566 2583701 0.05036005957052633 0.33447984074394754 chrMT 16571 160568 9.68969887152254 6.676433409917355 chrX 155270560 10397097 0.06696116121433451 0.45477425986427145 chrY 59373566 4373276 0.07365695366857365 1.6789028942698387