BamQC report ----------------------------------- >>>>>>> Input bam file = SRR1006182.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 = 6,558,948 number of mapped reads = 1,319,458 (20.12%) number of secondary alignments = 0 number of mapped paired reads (first in pair) = 660,472 number of mapped paired reads (second in pair) = 658,986 number of mapped paired reads (both in pair) = 1,143,004 number of mapped paired reads (singletons) = 176,454 number of mapped bases = 51,052,678 bp number of sequenced bases = 51,044,800 bp number of aligned bases = 0 bp number of duplicated reads (estimated) = 42,894 duplication rate = 2.43% >>>>>>> Insert size mean insert size = 69,542.7223 std insert size = 2,484,872.148 median insert size = 141 >>>>>>> Mapping quality mean mapping quality = 47.4255 >>>>>>> ACTG content number of A's = 14,139,200 bp (27.7%) number of C's = 11,107,787 bp (21.76%) number of T's = 14,413,798 bp (28.24%) number of G's = 11,382,151 bp (22.3%) number of N's = 1,864 bp (0%) GC percentage = 44.06% >>>>>>> Mismatches and indels general error rate = 0.0029 number of mismatches = 147,964 number of insertions = 1,833 mapped reads with insertion percentage = 0.14% number of deletions = 5,777 mapped reads with deletion percentage = 0.44% homopolymer indels = 40.66% >>>>>>> Coverage mean coverageData = 0.0165X std coverageData = 0.3085X There is a 1.51% of reference with a coverageData >= 1X There is a 0.11% 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 4140124 0.0166102855968411 0.24013830509478634 chr2 243199373 4407401 0.018122583728865122 0.6119419743906929 chr3 198022430 3338112 0.0168572418791144 0.13826551899298506 chr4 191154276 3073553 0.016078913139248845 0.1428157323019652 chr5 180915260 3077668 0.017011655069892943 0.8148799167848141 chr6 171115067 2881051 0.016836921789008797 0.26159722268344954 chr7 159138663 2696439 0.016943959118218808 0.15506749218903426 chr8 146364022 2563091 0.01751175572368461 0.22610906827757862 chr9 141213431 2130702 0.015088522280858682 0.13607487424428333 chr10 135534747 2441015 0.018010252381996182 0.17713795728006412 chr11 135006516 2386322 0.017675606116670694 0.19132804374611212 chr12 133851895 2277083 0.017011959374949454 0.13948218921695846 chr13 115169878 1556700 0.013516555083960408 0.1243157010751557 chr14 107349540 1611126 0.015008224534543884 0.17419160655670501 chr15 102531392 1431706 0.013963586878836094 0.12573624606166353 chr16 90354753 1622177 0.017953421885841467 0.15435366944361975 chr17 81195210 1488038 0.01832667222610792 0.18079700294966838 chr18 78077248 1314097 0.0168307289724146 0.16820210222377666 chr19 59128983 1169855 0.01978479826044023 0.16733112302269884 chr20 63025520 1172380 0.018601671196048837 0.1491486573360536 chr21 48129895 676094 0.014047277684690565 0.2398382711527177 chr22 51304566 711608 0.013870266439833055 0.1272201740193257 chrMT 16571 3266 0.19709130408545047 0.46689318513480416 chrX 155270560 2751117 0.01771821393572613 0.14606603417406272 chrY 59373566 131953 0.0022224199907413342 0.07203055500755824