BamQC report ----------------------------------- >>>>>>> Input bam file = SRR1549029.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 = 7,753,173 number of mapped reads = 6,827,953 (88.07%) number of secondary alignments = 0 number of mapped bases = 269,151,799 bp number of sequenced bases = 269,126,003 bp number of aligned bases = 0 bp number of duplicated reads (estimated) = 385,420 duplication rate = 2.99% >>>>>>> Insert size mean insert size = 0 std insert size = 0 median insert size = 0 >>>>>>> Mapping quality mean mapping quality = 32.2147 >>>>>>> ACTG content number of A's = 74,635,871 bp (27.73%) number of C's = 59,179,932 bp (21.99%) number of T's = 75,885,684 bp (28.2%) number of G's = 59,421,846 bp (22.08%) number of N's = 2,670 bp (0%) GC percentage = 44.07% >>>>>>> Mismatches and indels general error rate = 0.0039 number of mismatches = 1,037,990 number of insertions = 11,213 mapped reads with insertion percentage = 0.16% number of deletions = 20,863 mapped reads with deletion percentage = 0.31% homopolymer indels = 36.3% >>>>>>> Coverage mean coverageData = 0.0869X std coverageData = 1.2089X There is a 7.04% of reference with a coverageData >= 1X There is a 1.07% of reference with a coverageData >= 2X There is a 0.2% 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 0.01% 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% 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 21291965 0.08542391956568084 1.575409445529187 chr2 243199373 22526249 0.09262461790968515 1.210926805516727 chr3 198022430 17538291 0.0885671941304831 0.36916044844692164 chr4 191154276 16777275 0.08776824328010324 0.3814092109987685 chr5 180915260 16148157 0.08925812559979739 0.41125146614672814 chr6 171115067 15311695 0.08948186310209609 0.46502216648077244 chr7 159138663 15538255 0.09763972316394288 1.6575963019011517 chr8 146364022 13754935 0.09397756915972151 3.178820520439718 chr9 141213431 11434835 0.08097554828194777 1.3164365039919446 chr10 135534747 12294212 0.09070893089873108 0.7485841972783418 chr11 135006516 12475175 0.09240424365887644 1.3682739215609088 chr12 133851895 12319753 0.09204018366717931 0.45102432282195926 chr13 115169878 8107395 0.07039509931581242 0.30456306636901 chr14 107349540 8181926 0.07621761583701243 0.6411537586345849 chr15 102531392 7611018 0.07423109987622133 0.33390625554792464 chr16 90354753 7660099 0.08477804150491121 0.5604061566852968 chr17 81195210 7541852 0.09288543006416265 0.500777898293397 chr18 78077248 7121473 0.09121060465655757 2.5618381739180776 chr19 59128983 6517439 0.11022410109776452 1.6871441342251932 chr20 63025520 5409795 0.08583499192073306 0.41709418101832607 chr21 48129895 3275283 0.06805090682204895 0.5211894857143694 chr22 51304566 3087956 0.060188716926286835 0.3499374844355922 chrMT 16571 26462 1.596886126365337 2.141663167503149 chrX 155270560 16016422 0.10315169855766605 0.7158708407565952 chrY 59373566 1183882 0.01993954683469745 0.2327863878026333