BamQC report ----------------------------------- >>>>>>> Input bam file = SRR6231788.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 = 5,656,610 number of mapped reads = 1,677,184 (29.65%) number of supplementary alignments = 19,264 (0.34%) number of secondary alignments = 0 number of mapped bases = 102,243,393 bp number of sequenced bases = 102,208,353 bp number of aligned bases = 0 bp number of duplicated reads (estimated) = 305,119 duplication rate = 10.75% >>>>>>> Insert size mean insert size = 0 std insert size = 0 median insert size = 0 >>>>>>> Mapping quality mean mapping quality = 43.4345 >>>>>>> ACTG content number of A's = 29,417,022 bp (28.78%) number of C's = 20,482,941 bp (20.04%) number of T's = 28,464,824 bp (27.85%) number of G's = 23,835,576 bp (23.32%) number of N's = 7,990 bp (0.01%) GC percentage = 43.36% >>>>>>> Mismatches and indels general error rate = 0.0065 number of mismatches = 642,869 number of insertions = 7,967 mapped reads with insertion percentage = 0.47% number of deletions = 22,034 mapped reads with deletion percentage = 1.3% homopolymer indels = 44.68% >>>>>>> Coverage mean coverageData = 0.033X std coverageData = 5.4566X There is a 1.42% of reference with a coverageData >= 1X There is a 0.72% of reference with a coverageData >= 2X There is a 0.41% of reference with a coverageData >= 3X There is a 0.24% of reference with a coverageData >= 4X There is a 0.14% of reference with a coverageData >= 5X There is a 0.09% of reference with a coverageData >= 6X There is a 0.05% of reference with a coverageData >= 7X There is a 0.03% of reference with a coverageData >= 8X There is a 0.02% of reference with a coverageData >= 9X There is a 0.02% 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% 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 8792828 0.03527705553840927 0.4617612336085606 chr2 243199373 8410651 0.03458335807469372 19.416327771067536 chr3 198022430 3872940 0.019558087434842608 0.269582001018167 chr4 191154276 14436859 0.07552464586248649 0.5630396232416425 chr5 180915260 5259744 0.029072970406144844 0.3314807633725148 chr6 171115067 4128830 0.024128968140485256 0.3174613560078684 chr7 159138663 8394156 0.0527474332243196 0.5200710475930083 chr8 146364022 4385234 0.029961147145847085 0.3769869522612678 chr9 141213431 6453025 0.04569696348501015 0.5391786876052407 chr10 135534747 3086377 0.022771850527746954 0.432775749040349 chr11 135006516 4789443 0.03547564326450732 0.4047854604687559 chr12 133851895 5064985 0.03784021884785419 0.3949038407261431 chr13 115169878 2446681 0.021244105164372928 0.2979597510582218 chr14 107349540 3074741 0.02864233046550549 0.44299829553287184 chr15 102531392 2498931 0.024372350274928484 0.3070344850397168 chr16 90354753 2448390 0.02709752302681852 0.3630606260717802 chr17 81195210 4743863 0.058425404651333494 0.4780199365946618 chr18 78077248 1460227 0.018702336947121905 0.6732246540445815 chr19 59128983 1209428 0.020454063957095286 0.3689471751426353 chr20 63025520 1109186 0.01759899799319387 0.2764602513241048 chr21 48129895 1239530 0.025753847998214 0.37559558075238 chr22 51304566 1431910 0.027909991481070127 0.31959038561821235 chrMT 16571 51781 3.1247963309395934 3.4839578142149827 chrX 155270560 3185446 0.02051545379883991 0.3150789683810247 chrY 59373566 268207 0.004517279625751298 0.20275665065330406