BamQC report ----------------------------------- >>>>>>> Input bam file = SRR6238048.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 = 1,836,316 number of mapped reads = 497,713 (27.1%) number of supplementary alignments = 3,498 (0.19%) number of secondary alignments = 0 number of mapped bases = 29,546,969 bp number of sequenced bases = 29,532,850 bp number of aligned bases = 0 bp number of duplicated reads (estimated) = 54,292 duplication rate = 9.18% >>>>>>> Insert size mean insert size = 0 std insert size = 0 median insert size = 0 >>>>>>> Mapping quality mean mapping quality = 44.5681 >>>>>>> ACTG content number of A's = 7,680,800 bp (26.01%) number of C's = 5,051,306 bp (17.1%) number of T's = 9,590,867 bp (32.48%) number of G's = 7,208,622 bp (24.41%) number of N's = 1,255 bp (0%) GC percentage = 41.51% >>>>>>> Mismatches and indels general error rate = 0.0086 number of mismatches = 250,945 number of insertions = 2,379 mapped reads with insertion percentage = 0.47% number of deletions = 9,171 mapped reads with deletion percentage = 1.82% homopolymer indels = 46.36% >>>>>>> Coverage mean coverageData = 0.0095X std coverageData = 0.148X There is a 0.69% of reference with a coverageData >= 1X There is a 0.17% of reference with a coverageData >= 2X There is a 0.05% of reference with a coverageData >= 3X There is a 0.02% 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 2568242 0.01030385396712813 0.16726796067001323 chr2 243199373 2512870 0.010332551309661478 0.21508895245343426 chr3 198022430 1976923 0.009983328656253738 0.13723692723240843 chr4 191154276 1868204 0.009773278626526775 0.1356596321379733 chr5 180915260 1816035 0.010038042119830025 0.1360126466544724 chr6 171115067 1732954 0.010127419112660605 0.14987960039699968 chr7 159138663 1619340 0.010175654171481885 0.15292741672357227 chr8 146364022 1563019 0.010678983664441798 0.15789890470923731 chr9 141213431 1251832 0.0088648224969479 0.13278577459799668 chr10 135534747 1362437 0.010052307841029135 0.14548202490150774 chr11 135006516 1346350 0.009972481624516553 0.13983431420614986 chr12 133851895 1316520 0.009835647078436954 0.1365061414266568 chr13 115169878 929693 0.008072362462691851 0.12370543745985535 chr14 107349540 890247 0.008292974520431108 0.12553981883054752 chr15 102531392 790040 0.007705347451051869 0.1198572947404323 chr16 90354753 870628 0.00963566354943165 0.1339556208316017 chr17 81195210 767281 0.009449830845932906 0.12992564324929767 chr18 78077248 764785 0.009795235098450192 0.1782007608978028 chr19 59128983 566058 0.009573274750895006 0.14311216806983615 chr20 63025520 650982 0.010328863609534677 0.13853548968922863 chr21 48129895 388867 0.008079531442983618 0.12109086743190164 chr22 51304566 307992 0.006003208369407121 0.10350945485930417 chrMT 16571 19526 1.1783235773338965 1.8904936362329172 chrX 155270560 1572941 0.010130323481798481 0.13807270418124507 chrY 59373566 93203 0.001569772649330175 0.05270211137984072