BamQC report ----------------------------------- >>>>>>> Input bam file = SRR9716851.sorted.bam outfile = /home/luna/rawdata/yangyxdownload/SRP215441/SRP215441.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 = 876,892 number of mapped reads = 774,146 (88.28%) number of supplementary alignments = 3,458 (0.39%) number of secondary alignments = 0 number of mapped bases = 44,602,582 bp number of sequenced bases = 44,589,166 bp number of aligned bases = 0 bp number of duplicated reads (estimated) = 16,336 duplication rate = 1.51% >>>>>>> Insert size mean insert size = 0 std insert size = 0 median insert size = 0 >>>>>>> Mapping quality mean mapping quality = 44.2505 >>>>>>> ACTG content number of A's = 10,660,856 bp (23.91%) number of C's = 8,718,128 bp (19.55%) number of T's = 14,629,582 bp (32.81%) number of G's = 10,580,325 bp (23.73%) number of N's = 275 bp (0%) GC percentage = 43.28% >>>>>>> Mismatches and indels general error rate = 0.0052 number of mismatches = 226,932 number of insertions = 3,325 mapped reads with insertion percentage = 0.43% number of deletions = 8,461 mapped reads with deletion percentage = 1.09% homopolymer indels = 41.74% >>>>>>> Coverage mean coverageData = 0.0144X std coverageData = 0.1594X There is a 1.36% of reference with a coverageData >= 1X There is a 0.06% 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 5290381 0.021225146716886214 0.24011223936395917 chr2 243199373 4621474 0.01900282037322522 0.22511834222429034 chr3 198022430 2850106 0.014392844285367067 0.12532045333216488 chr4 191154276 1873099 0.009798886214818444 0.10853054064596528 chr5 180915260 3246646 0.017945672465661547 0.13951131567946318 chr6 171115067 1667803 0.009746675317609524 0.11046375656052802 chr7 159138663 3031803 0.019051328840182603 0.24000047389238904 chr8 146364022 1984519 0.013558789741375104 0.13605176569489716 chr9 141213431 1229847 0.008709136172748327 0.1175622533325576 chr10 135534747 2022730 0.01492406961884099 0.14452893318228152 chr11 135006516 1941348 0.014379661497227289 0.15192276146246994 chr12 133851895 1795656 0.013415245260442521 0.12136198526779977 chr13 115169878 1314589 0.011414347421640925 0.11160446830574755 chr14 107349540 653198 0.006084776888657371 0.0846323723546374 chr15 102531392 1936002 0.018882041511735254 0.14546839405741607 chr16 90354753 1321528 0.014625993167177382 0.1315283366138197 chr17 81195210 1664323 0.020497797838074438 0.1546755444780897 chr18 78077248 1457957 0.018673263176489006 0.24125536329716268 chr19 59128983 699913 0.011837054596389727 0.18253568141408083 chr20 63025520 1150683 0.018257413822210432 0.14114092524514962 chr21 48129895 564442 0.011727472083618715 0.11452901061799065 chr22 51304566 503753 0.009818872651607656 0.10247297906980422 chrMT 16571 2450 0.1478486512582222 0.4089301346575851 chrX 155270560 1677480 0.01080359341783787 0.11977177060253402 chrY 59373566 100852 0.0016986010238967287 0.052978483419092275