BamQC report ----------------------------------- >>>>>>> Input bam file = SRR3080692.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 = 2,800,294 number of mapped reads = 2,489,469 (88.9%) number of supplementary alignments = 27,510 (0.98%) number of secondary alignments = 0 number of mapped bases = 175,774,845 bp number of sequenced bases = 175,705,098 bp number of aligned bases = 0 bp number of duplicated reads (estimated) = 139,299 duplication rate = 4.39% >>>>>>> Insert size mean insert size = 0 std insert size = 0 median insert size = 0 >>>>>>> Mapping quality mean mapping quality = 48.1864 >>>>>>> ACTG content number of A's = 53,327,433 bp (30.35%) number of C's = 32,481,615 bp (18.49%) number of T's = 54,768,362 bp (31.17%) number of G's = 35,124,914 bp (19.99%) number of N's = 2,774 bp (0%) GC percentage = 38.48% >>>>>>> Mismatches and indels general error rate = 0.0083 number of mismatches = 1,420,218 number of insertions = 14,617 mapped reads with insertion percentage = 0.58% number of deletions = 38,335 mapped reads with deletion percentage = 1.52% homopolymer indels = 47.17% >>>>>>> Coverage mean coverageData = 0.0568X std coverageData = 0.6191X There is a 3.81% of reference with a coverageData >= 1X There is a 1.18% of reference with a coverageData >= 2X There is a 0.39% of reference with a coverageData >= 3X There is a 0.13% of reference with a coverageData >= 4X There is a 0.05% of reference with a coverageData >= 5X There is a 0.02% of reference with a coverageData >= 6X There is a 0.01% of reference with a coverageData >= 7X There is a 0.01% 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 12293806 0.04932307069357312 0.7057153219156985 chr2 243199373 15573256 0.06403493482690846 0.4958337554803889 chr3 198022430 11155330 0.05633366886771362 0.3276836621427037 chr4 191154276 11722385 0.06132421018926095 0.3781181905551052 chr5 180915260 10433071 0.05766827519137965 0.3331327122141526 chr6 171115067 10566772 0.06175243469355039 0.35692779601271224 chr7 159138663 9318661 0.05855686370822406 0.8135825438912886 chr8 146364022 9951339 0.06799033576707805 1.9366406995445802 chr9 141213431 7483078 0.052991262566235646 0.4582747657893618 chr10 135534747 8960340 0.06611101727293592 0.45886079539175467 chr11 135006516 8118016 0.0601305495506602 0.40754356961339455 chr12 133851895 7557447 0.056461262651529884 0.33317682310414504 chr13 115169878 6113036 0.05307842732975718 0.3205804281917762 chr14 107349540 5686872 0.05297528056477932 0.34106096407377456 chr15 102531392 4832950 0.04713629558447817 0.2972132745424056 chr16 90354753 4280785 0.04737752976868854 0.32704644343205663 chr17 81195210 4055949 0.04995305757568704 0.34529443404571475 chr18 78077248 5437219 0.0696389683201949 0.7768567355716675 chr19 59128983 2849521 0.04819161188684744 0.4736182522568551 chr20 63025520 3330323 0.05284086509718603 0.3236453857736613 chr21 48129895 2654060 0.05514368980027901 0.35850222463754966 chr22 51304566 1844150 0.035945143751922586 0.25020540399996455 chrMT 16571 254630 15.366000844849436 9.076557551456522 chrX 155270560 10828685 0.0697407480207452 0.4000097283094345 chrY 59373566 473164 0.00796927036519922 0.22413054559572868