BamQC report ----------------------------------- >>>>>>> Input bam file = SRR1708612.sorted.bam outfile = /home/luna/rawdata/yangyxdownload/SRP051114/SRP051114.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 = 2,650,536 number of mapped reads = 1,606,687 (60.62%) number of supplementary alignments = 413 (0.02%) number of secondary alignments = 0 number of mapped bases = 77,356,871 bp number of sequenced bases = 77,336,593 bp number of aligned bases = 0 bp number of duplicated reads (estimated) = 69,179 duplication rate = 3.49% >>>>>>> Insert size mean insert size = 0 std insert size = 0 median insert size = 0 >>>>>>> Mapping quality mean mapping quality = 41.5909 >>>>>>> ACTG content number of A's = 22,358,170 bp (28.91%) number of C's = 14,729,897 bp (19.05%) number of T's = 24,209,479 bp (31.3%) number of G's = 16,032,372 bp (20.73%) number of N's = 6,675 bp (0.01%) GC percentage = 39.78% >>>>>>> Mismatches and indels general error rate = 0.0069 number of mismatches = 524,632 number of insertions = 3,927 mapped reads with insertion percentage = 0.24% number of deletions = 13,044 mapped reads with deletion percentage = 0.81% homopolymer indels = 49% >>>>>>> Coverage mean coverageData = 0.025X std coverageData = 0.2451X There is a 1.81% of reference with a coverageData >= 1X There is a 0.44% of reference with a coverageData >= 2X There is a 0.14% of reference with a coverageData >= 3X There is a 0.05% of reference with a coverageData >= 4X There is a 0.02% of reference with a coverageData >= 5X There is a 0.01% 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 6077106 0.024381507960214873 0.30240924851743817 chr2 243199373 6565481 0.026996290816917526 0.2792665156946268 chr3 198022430 4848557 0.024484887898810252 0.21022171764647232 chr4 191154276 5302032 0.02773692595817213 0.2301915951769663 chr5 180915260 5097145 0.028174212612026205 0.2269440940669013 chr6 171115067 4859788 0.028400701850527284 0.25763511613365364 chr7 159138663 4500834 0.028282467096006708 0.3060520785377392 chr8 146364022 4083976 0.027902868096915237 0.261681346028657 chr9 141213431 3229544 0.022869949247249718 0.23405854945054919 chr10 135534747 3877517 0.02860902525608433 0.2446752228745578 chr11 135006516 3333243 0.024689497209156926 0.24766813799010318 chr12 133851895 3883699 0.029014897398352113 0.23277649592892014 chr13 115169878 2137629 0.018560660453248026 0.18512975759858227 chr14 107349540 2297515 0.021402187657254983 0.20159169312599623 chr15 102531392 2230659 0.021755863804131324 0.19857039663552198 chr16 90354753 1830533 0.020259399082193274 0.19158151098588438 chr17 81195210 1998423 0.02461257258894952 0.22399762948155807 chr18 78077248 2164117 0.027717639330730508 0.3369185132503243 chr19 59128983 1408464 0.023820196603077038 0.29406549966128487 chr20 63025520 1416144 0.022469374310596722 0.20616193167289748 chr21 48129895 1018026 0.02115163558948134 0.1999926710880786 chr22 51304566 604603 0.01178458463131722 0.14124153055251243 chrMT 16571 2803 0.1691509263170599 0.48331461922170066 chrX 155270560 4386859 0.028252999151931957 0.23408639527392627 chrY 59373566 202174 0.0034051180284505734 0.08763755744860545