BamQC report ----------------------------------- >>>>>>> Input bam file = SRR1548961.sorted.bam outfile = /home/luna/rawdata/yangyxdownload/SRP041670/SRP041670.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 = 9,163,169 number of mapped reads = 7,890,434 (86.11%) number of secondary alignments = 0 number of mapped bases = 311,184,531 bp number of sequenced bases = 311,156,315 bp number of aligned bases = 0 bp number of duplicated reads (estimated) = 479,636 duplication rate = 3.52% >>>>>>> Insert size mean insert size = 0 std insert size = 0 median insert size = 0 >>>>>>> Mapping quality mean mapping quality = 31.9316 >>>>>>> ACTG content number of A's = 85,037,507 bp (27.33%) number of C's = 69,989,311 bp (22.49%) number of T's = 86,548,560 bp (27.82%) number of G's = 69,580,529 bp (22.36%) number of N's = 408 bp (0%) GC percentage = 44.86% >>>>>>> Mismatches and indels general error rate = 0.0037 number of mismatches = 1,146,026 number of insertions = 12,443 mapped reads with insertion percentage = 0.16% number of deletions = 22,526 mapped reads with deletion percentage = 0.29% homopolymer indels = 35.65% >>>>>>> Coverage mean coverageData = 0.1005X std coverageData = 1.1729X There is a 7.88% of reference with a coverageData >= 1X There is a 1.38% of reference with a coverageData >= 2X There is a 0.3% of reference with a coverageData >= 3X There is a 0.09% of reference with a coverageData >= 4X There is a 0.04% 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 0.01% of reference with a coverageData >= 9X There is a 0.01% 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 0.01% of reference with a coverageData >= 14X There is a 0.01% of reference with a coverageData >= 15X There is a 0.01% 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 25208002 0.1011351622670581 2.0980081517535543 chr2 243199373 26405323 0.10857479883387693 1.2342803128179658 chr3 198022430 20326114 0.10264551344006838 0.3997605717909143 chr4 191154276 20056188 0.10492147191099194 0.5188016580622246 chr5 180915260 18649929 0.10308654449602538 0.43345222228130503 chr6 171115067 17759612 0.10378754081310677 0.44757574563357766 chr7 159138663 17973329 0.11294130955467434 1.8630739715462472 chr8 146364022 16002384 0.10933277031701137 2.0262078654474363 chr9 141213431 13420334 0.09503581851219237 1.2922255742472641 chr10 135534747 14855632 0.10960755325717324 0.9623550168608047 chr11 135006516 14297519 0.10590243659054205 0.7827537627407916 chr12 133851895 14328897 0.10705038580141132 0.48066729443327794 chr13 115169878 9443734 0.08199829820085422 0.3384028619344181 chr14 107349540 9453881 0.0880663391757431 0.6185348030961116 chr15 102531392 8715343 0.08500170367334914 0.3693451905495629 chr16 90354753 9256270 0.10244364233943509 0.5858078646898751 chr17 81195210 9144313 0.11262133566746117 0.4746932051965292 chr18 78077248 8172461 0.10467147868736357 2.4811889101298292 chr19 59128983 8098247 0.1369590104399394 2.1958810309194354 chr20 63025520 6481728 0.10284291188712127 0.484716336536844 chr21 48129895 3924722 0.08154437070764439 0.6103648675761875 chr22 51304566 3900707 0.07603040633849237 0.5270617741603449 chrMT 16571 7022 0.4237523384225454 0.843151979760353 chrX 155270560 12271456 0.0790327284193475 0.6463537918666856 chrY 59373566 3031384 0.05105612150700196 0.5199828280861094