BamQC report ----------------------------------- >>>>>>> Input bam file = SRR1819039.sorted.bam outfile = /home/luna/rawdata/yangyxdownload/SRP055057/SRP055057.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 = 827,813 number of mapped reads = 713,012 (86.13%) number of supplementary alignments = 2,941 (0.36%) number of secondary alignments = 0 number of mapped bases = 40,415,956 bp number of sequenced bases = 40,405,528 bp number of aligned bases = 0 bp number of duplicated reads (estimated) = 13,021 duplication rate = 1.41% >>>>>>> Insert size mean insert size = 0 std insert size = 0 median insert size = 0 >>>>>>> Mapping quality mean mapping quality = 43.6444 >>>>>>> ACTG content number of A's = 9,810,416 bp (24.28%) number of C's = 8,377,883 bp (20.73%) number of T's = 12,745,008 bp (31.54%) number of G's = 9,471,412 bp (23.44%) number of N's = 809 bp (0%) GC percentage = 44.18% >>>>>>> Mismatches and indels general error rate = 0.005 number of mismatches = 196,493 number of insertions = 3,180 mapped reads with insertion percentage = 0.44% number of deletions = 6,177 mapped reads with deletion percentage = 0.86% homopolymer indels = 38.79% >>>>>>> Coverage mean coverageData = 0.0131X std coverageData = 0.1351X There is a 1.23% 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 4657877 0.01868752415264795 0.18980823712270212 chr2 243199373 3721004 0.015300220366933265 0.1541946806967398 chr3 198022430 2514151 0.0126962940511335 0.1181040535782031 chr4 191154276 2692409 0.014085005349291795 0.1302998445432803 chr5 180915260 1947545 0.010764957030158761 0.11003134097898601 chr6 171115067 2024575 0.0118316582840715 0.11786843171477693 chr7 159138663 1520192 0.009552625184490836 0.11343040868898983 chr8 146364022 2374306 0.016221923718384837 0.1422249056292299 chr9 141213431 1247313 0.008832821291623457 0.12022561109400144 chr10 135534747 1958554 0.01445056742534075 0.15008463155729415 chr11 135006516 1335723 0.00989376690529515 0.11883238282568048 chr12 133851895 1778131 0.013284316968392565 0.12129819601956345 chr13 115169878 1295038 0.011244589492401823 0.11023537499738477 chr14 107349540 1568018 0.014606657839428097 0.12927428542274347 chr15 102531392 1331723 0.012988441627711443 0.11916001051464468 chr16 90354753 1123982 0.012439655498809233 0.12281056528968062 chr17 81195210 702988 0.008657998421335446 0.09933380082806423 chr18 78077248 1029239 0.013182316569354494 0.20265555334779484 chr19 59128983 777484 0.01314894930629874 0.15001696709262588 chr20 63025520 1370899 0.021751490507337344 0.15719015863181768 chr21 48129895 566388 0.01176790433471754 0.11981434290968586 chr22 51304566 574161 0.011191226137650204 0.11154127552940954 chrMT 16571 3858 0.23281636594049845 0.5174986642995718 chrX 155270560 2173583 0.013998680754419898 0.13065897780706037 chrY 59373566 126815 0.002135883163898224 0.061654905293298715