BamQC report ----------------------------------- >>>>>>> Input bam file = SRR6008763.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 = 1,447,857 number of mapped reads = 1,294,529 (89.41%) number of supplementary alignments = 9,059 (0.63%) number of secondary alignments = 0 number of mapped bases = 85,839,366 bp number of sequenced bases = 85,795,510 bp number of aligned bases = 0 bp number of duplicated reads (estimated) = 53,126 duplication rate = 3.25% >>>>>>> Insert size mean insert size = 0 std insert size = 0 median insert size = 0 >>>>>>> Mapping quality mean mapping quality = 45.2232 >>>>>>> ACTG content number of A's = 22,898,923 bp (26.69%) number of C's = 16,507,968 bp (19.24%) number of T's = 26,579,430 bp (30.98%) number of G's = 19,698,760 bp (22.96%) number of N's = 110,429 bp (0.13%) GC percentage = 42.2% >>>>>>> Mismatches and indels general error rate = 0.0085 number of mismatches = 713,053 number of insertions = 6,196 mapped reads with insertion percentage = 0.47% number of deletions = 24,760 mapped reads with deletion percentage = 1.89% homopolymer indels = 44.99% >>>>>>> Coverage mean coverageData = 0.0277X std coverageData = 0.2767X There is a 2.31% of reference with a coverageData >= 1X There is a 0.33% of reference with a coverageData >= 2X There is a 0.06% of reference with a coverageData >= 3X There is a 0.01% 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 7733731 0.031027930718776423 0.4266844709842534 chr2 243199373 8347280 0.03432278585685334 0.3593048739264646 chr3 198022430 6765316 0.03416439238726643 0.2310908131525304 chr4 191154276 4344471 0.022727563782041684 0.1824565681526844 chr5 180915260 3207245 0.017727885419947437 0.15404359294623318 chr6 171115067 4548233 0.026579967969740503 0.20444213065852176 chr7 159138663 4264582 0.026797900143222895 0.28050891742915895 chr8 146364022 6898758 0.047134247240076525 0.3536422150221963 chr9 141213431 2451145 0.017357732778265262 0.1914806565097791 chr10 135534747 5316011 0.039222495468265416 0.4180982365159578 chr11 135006516 3801112 0.028155026235918864 0.22651048951279432 chr12 133851895 3439106 0.0256933680318833 0.18429622350748398 chr13 115169878 1841803 0.015992054797522665 0.14773803247841247 chr14 107349540 2763491 0.02574292353744599 0.18817987950198153 chr15 102531392 2082986 0.020315592711352245 0.16327491025578092 chr16 90354753 2322870 0.025708332133894493 0.23690579877381193 chr17 81195210 2801189 0.03449943660469626 0.24023129833152482 chr18 78077248 1415409 0.018128315690634996 0.2820919833274593 chr19 59128983 2306260 0.03900388410198092 0.3190852124256057 chr20 63025520 2223954 0.035286563284206145 0.2190266543550873 chr21 48129895 909359 0.018893849654149465 0.1647922502958171 chr22 51304566 1397538 0.027240031618238424 0.19176247263730212 chrMT 16571 457081 27.58318749622835 15.27790489848914 chrX 155270560 3974264 0.025595734310483585 0.1945049359727904 chrY 59373566 226172 0.003809304632300509 0.1268170013935051