BamQC report ----------------------------------- >>>>>>> Input bam file = SRR3080717.sorted.bam outfile = /home/luna/rawdata/yangyxdownload/SRP064210/SRP064210.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 = 2,098,090 number of mapped reads = 1,883,667 (89.78%) number of supplementary alignments = 11,883 (0.57%) number of secondary alignments = 0 number of mapped bases = 126,476,276 bp number of sequenced bases = 126,430,218 bp number of aligned bases = 0 bp number of duplicated reads (estimated) = 99,603 duplication rate = 4.47% >>>>>>> Insert size mean insert size = 0 std insert size = 0 median insert size = 0 >>>>>>> Mapping quality mean mapping quality = 46.063 >>>>>>> ACTG content number of A's = 35,117,987 bp (27.78%) number of C's = 23,266,969 bp (18.4%) number of T's = 40,345,018 bp (31.91%) number of G's = 27,698,416 bp (21.91%) number of N's = 1,828 bp (0%) GC percentage = 40.31% >>>>>>> Mismatches and indels general error rate = 0.0083 number of mismatches = 1,027,034 number of insertions = 8,988 mapped reads with insertion percentage = 0.47% number of deletions = 26,077 mapped reads with deletion percentage = 1.37% homopolymer indels = 48.06% >>>>>>> Coverage mean coverageData = 0.0409X std coverageData = 0.3608X There is a 3.44% of reference with a coverageData >= 1X There is a 0.47% of reference with a coverageData >= 2X There is a 0.08% of reference with a coverageData >= 3X There is a 0.02% of reference with a coverageData >= 4X There is a 0.01% of reference with a coverageData >= 5X There is a 0% of reference with a coverageData >= 6X There is a 0% of reference with a coverageData >= 7X There is a 0% of reference with a coverageData >= 8X There is a 0% of reference with a coverageData >= 9X There is a 0% of reference with a coverageData >= 10X There is a 0% of reference with a coverageData >= 11X There is a 0% of reference with a coverageData >= 12X There is a 0% of reference with a coverageData >= 13X There is a 0% of reference with a coverageData >= 14X There is a 0% of reference with a coverageData >= 15X There is a 0% of reference with a coverageData >= 16X There is a 0% of reference with a coverageData >= 17X There is a 0% 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 15097407 0.060571191114504784 0.5048019972540213 chr2 243199373 8361842 0.03438266265596005 0.33078622394447493 chr3 198022430 7873528 0.039760788714692574 0.2263253285161232 chr4 191154276 5489566 0.028717986931142466 0.20094234513232304 chr5 180915260 5719100 0.03161203759152213 0.2014848522321496 chr6 171115067 7510728 0.04389285018367202 0.33171362861240716 chr7 159138663 8136819 0.05113037175635942 0.9323355853474623 chr8 146364022 14823664 0.10127942507619803 0.4738784597480583 chr9 141213431 3972618 0.028132012457087033 0.24887890201699042 chr10 135534747 6130726 0.045233610831914565 0.329247513793081 chr11 135006516 5169539 0.03829103330094082 0.24681628135896433 chr12 133851895 4040393 0.030185549483628903 0.19957471978383715 chr13 115169878 2679104 0.023262193609339413 0.17323977268467555 chr14 107349540 2538727 0.02364916514779663 0.18056111029692554 chr15 102531392 2234608 0.021794378837653935 0.16787746641612097 chr16 90354753 3177496 0.035166893765953854 0.2251605852365842 chr17 81195210 1991339 0.024525326062953715 0.1875204283328187 chr18 78077248 4068150 0.052104167400982164 0.38009639131125295 chr19 59128983 2065013 0.03492387142866976 0.3366048037309582 chr20 63025520 3123087 0.049552736732675906 0.2585051965886944 chr21 48129895 1959018 0.04070272748361491 0.23777888725512172 chr22 51304566 1226825 0.02391258898866818 0.17322987637225673 chrMT 16571 168780 10.185263411984792 5.656642198556662 chrX 155270560 8628117 0.05556827385693721 0.28914195229896544 chrY 59373566 290082 0.004885709576547921 0.1030330838513053