BamQC report ----------------------------------- >>>>>>> Input bam file = SRR1006444.sorted.bam outfile = /home/luna/rawdata/yangyxdownload/SRP030642/SRP030642.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 = 1,379,277 number of mapped reads = 1,316,330 (95.44%) number of supplementary alignments = 4,361 (0.32%) number of secondary alignments = 0 number of mapped bases = 74,527,689 bp number of sequenced bases = 74,502,342 bp number of aligned bases = 0 bp number of duplicated reads (estimated) = 25,267 duplication rate = 1.41% >>>>>>> Insert size mean insert size = 0 std insert size = 0 median insert size = 0 >>>>>>> Mapping quality mean mapping quality = 46.2168 >>>>>>> ACTG content number of A's = 21,475,115 bp (28.82%) number of C's = 15,475,804 bp (20.77%) number of T's = 21,389,107 bp (28.71%) number of G's = 16,160,151 bp (21.69%) number of N's = 2,165 bp (0%) GC percentage = 42.46% >>>>>>> Mismatches and indels general error rate = 0.0045 number of mismatches = 327,199 number of insertions = 4,612 mapped reads with insertion percentage = 0.35% number of deletions = 15,277 mapped reads with deletion percentage = 1.16% homopolymer indels = 45.28% >>>>>>> Coverage mean coverageData = 0.0241X std coverageData = 0.2192X There is a 2.23% of reference with a coverageData >= 1X There is a 0.13% of reference with a coverageData >= 2X There is a 0.01% 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 6165078 0.0247344539213806 0.28232393319858906 chr2 243199373 6461429 0.02656844431913893 0.1973016091321693 chr3 198022430 5095500 0.025731933498644572 0.1681452869220071 chr4 191154276 4421168 0.0231287946705414 0.16510446277832586 chr5 180915260 4638837 0.025640938193936764 0.16803101150403008 chr6 171115067 4380692 0.02560085489140474 0.1758946970649165 chr7 159138663 4166190 0.026179621730264255 0.2263848530737138 chr8 146364022 3643034 0.02489022882959584 0.5227201471530301 chr9 141213431 3205674 0.02270091433441625 0.17903519056970416 chr10 135534747 3631052 0.026790561685262896 0.21411819365328058 chr11 135006516 3431401 0.02541655841263247 0.18696689116042153 chr12 133851895 3415792 0.025519190445529367 0.1686662906966529 chr13 115169878 2404636 0.020879035749260758 0.1511082866708752 chr14 107349540 2332506 0.021728141545832427 0.15811084579080217 chr15 102531392 2252505 0.021968930256989 0.15563717440256378 chr16 90354753 2305250 0.025513323023527053 0.18406274757139846 chr17 81195210 2037816 0.02509773667683106 0.17828775040008774 chr18 78077248 2019541 0.02586593472146969 0.25261151215489414 chr19 59128983 1509499 0.025528918703032658 0.2299269203850211 chr20 63025520 1663794 0.026398734988620484 0.17275638820750483 chr21 48129895 1433201 0.029777771175274744 0.1923619390183803 chr22 51304566 945247 0.018424227582394908 0.14948580129563513 chrMT 16571 40650 2.453080683121115 2.081488562112632 chrX 155270560 2273789 0.014644044563244958 0.13221644477499161 chrY 59373566 653408 0.011005032104691169 0.16021950829909287