BamQC report ----------------------------------- >>>>>>> Input bam file = SRR6238061.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 = 1,949,865 number of mapped reads = 1,798,710 (92.25%) number of supplementary alignments = 9,286 (0.48%) number of secondary alignments = 0 number of mapped bases = 120,072,270 bp number of sequenced bases = 120,016,191 bp number of aligned bases = 0 bp number of duplicated reads (estimated) = 54,553 duplication rate = 1.96% >>>>>>> Insert size mean insert size = 0 std insert size = 0 median insert size = 0 >>>>>>> Mapping quality mean mapping quality = 44.1117 >>>>>>> ACTG content number of A's = 32,294,643 bp (26.91%) number of C's = 23,100,124 bp (19.25%) number of T's = 36,744,822 bp (30.62%) number of G's = 27,870,059 bp (23.22%) number of N's = 6,543 bp (0.01%) GC percentage = 42.47% >>>>>>> Mismatches and indels general error rate = 0.0076 number of mismatches = 889,486 number of insertions = 8,658 mapped reads with insertion percentage = 0.48% number of deletions = 31,809 mapped reads with deletion percentage = 1.75% homopolymer indels = 45.56% >>>>>>> Coverage mean coverageData = 0.0388X std coverageData = 0.3806X There is a 3.44% of reference with a coverageData >= 1X There is a 0.3% of reference with a coverageData >= 2X There is a 0.04% of reference with a coverageData >= 3X There is a 0.01% 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 10204266 0.04093978165053398 0.7020127388193352 chr2 243199373 10924899 0.04492157551738425 0.4549959356134935 chr3 198022430 7832733 0.03955477669878104 0.22041879502260633 chr4 191154276 7438319 0.03891264770870206 0.23896386893214003 chr5 180915260 5732207 0.03168448587476811 0.19864046086827455 chr6 171115067 6983186 0.04080988379591378 0.29161293877147565 chr7 159138663 6543244 0.04111662041549262 0.5471496169753045 chr8 146364022 6579337 0.04495187348705135 0.4104313387725406 chr9 141213431 5458501 0.03865426228472559 0.38840793237109483 chr10 135534747 6398759 0.047211207027228225 0.3939610543471053 chr11 135006516 6418354 0.04754106831406567 0.3465856250404994 chr12 133851895 5081587 0.037964251458673784 0.21986218398928883 chr13 115169878 3501821 0.03040570208817969 0.18922283670758572 chr14 107349540 2885026 0.02687506625552378 0.24374408799465036 chr15 102531392 3508869 0.034222387227513695 0.20495437291299204 chr16 90354753 3136594 0.03471421143722234 0.24369335764068858 chr17 81195210 3090432 0.03806175265757672 0.2540116104898609 chr18 78077248 3198579 0.040966851188197616 0.6783352912263427 chr19 59128983 2522104 0.04265427666834723 0.46336603294195977 chr20 63025520 2103360 0.03337314789310743 0.21223415817113023 chr21 48129895 1651494 0.0343132682919836 0.2456894917005153 chr22 51304566 1240402 0.024177224303973257 0.1681334581996465 chrMT 16571 25866 1.5609196789572144 1.552378488926015 chrX 155270560 7278246 0.046874603917188166 0.28498830385407065 chrY 59373566 334085 0.005626830633686378 0.16661791828939357