BamQC report ----------------------------------- >>>>>>> Input bam file = SRR6237591.sorted.bam outfile = /home/luna/rawdata/yangyxdownload/SRP116771/SRP116771.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 = 427,677 number of mapped reads = 285,430 (66.74%) number of supplementary alignments = 1,683 (0.39%) number of secondary alignments = 0 number of mapped bases = 18,170,182 bp number of sequenced bases = 18,160,057 bp number of aligned bases = 0 bp number of duplicated reads (estimated) = 5,125 duplication rate = 1.47% >>>>>>> Insert size mean insert size = 0 std insert size = 0 median insert size = 0 >>>>>>> Mapping quality mean mapping quality = 43.6332 >>>>>>> ACTG content number of A's = 5,206,825 bp (28.67%) number of C's = 3,306,638 bp (18.21%) number of T's = 5,425,644 bp (29.88%) number of G's = 4,190,914 bp (23.08%) number of N's = 30,036 bp (0.17%) GC percentage = 41.29% >>>>>>> Mismatches and indels general error rate = 0.0118 number of mismatches = 212,181 number of insertions = 1,702 mapped reads with insertion percentage = 0.59% number of deletions = 6,319 mapped reads with deletion percentage = 2.18% homopolymer indels = 46.09% >>>>>>> Coverage mean coverageData = 0.0059X std coverageData = 0.0883X There is a 0.55% of reference with a coverageData >= 1X There is a 0.03% of reference with a coverageData >= 2X There is a 0% of reference with a coverageData >= 3X There is a 0% of reference with a coverageData >= 4X There is a 0% 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 1525248 0.0061193348039843 0.10000483828723755 chr2 243199373 1571625 0.0064622905092769295 0.09807722019007602 chr3 198022430 1286669 0.0064975922172048894 0.08612680627205907 chr4 191154276 1204571 0.006301564501753547 0.08490314704672115 chr5 180915260 1037685 0.005735751644167551 0.07947818484890831 chr6 171115067 971969 0.005680206991941861 0.08095385785351317 chr7 159138663 1091618 0.006859539846705888 0.10824579999614713 chr8 146364022 991350 0.006773180911904703 0.09548554568156913 chr9 141213431 724043 0.0051272955757303285 0.08563914184260038 chr10 135534747 766073 0.005652225845819449 0.08517620970274808 chr11 135006516 775364 0.005743159833855723 0.0937709284711721 chr12 133851895 1077049 0.008046572668993592 0.09600869457649878 chr13 115169878 638521 0.005544166678721324 0.0788094608876972 chr14 107349540 507857 0.004730872624139796 0.07479153314932224 chr15 102531392 556540 0.0054279961399529226 0.07881894979836865 chr16 90354753 449555 0.004975443848537774 0.07797441040976685 chr17 81195210 402193 0.004953407965814732 0.07550059576776018 chr18 78077248 491504 0.00629509892561787 0.11638653054042575 chr19 59128983 279058 0.004719479108916857 0.08292589339707274 chr20 63025520 379092 0.006014896822747357 0.08294975726022878 chr21 48129895 222674 0.004626521624449835 0.07276408286687583 chr22 51304566 160145 0.0031214570648546176 0.058842122921086364 chrMT 16571 12590 0.7597610283024561 1.1057392408322777 chrX 155270560 986784 0.006355254982013332 0.08629536414586654 chrY 59373566 60405 0.0010173719395597698 0.036623518637894786