BamQC report ----------------------------------- >>>>>>> Input bam file = SRR6238279.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 = 1,517,401 number of mapped reads = 1,356,244 (89.38%) number of supplementary alignments = 16,848 (1.11%) number of secondary alignments = 0 number of mapped bases = 89,058,794 bp number of sequenced bases = 89,013,110 bp number of aligned bases = 0 bp number of duplicated reads (estimated) = 80,328 duplication rate = 5.07% >>>>>>> Insert size mean insert size = 0 std insert size = 0 median insert size = 0 >>>>>>> Mapping quality mean mapping quality = 44.0464 >>>>>>> ACTG content number of A's = 24,269,981 bp (27.27%) number of C's = 15,938,714 bp (17.91%) number of T's = 28,791,751 bp (32.35%) number of G's = 19,943,491 bp (22.41%) number of N's = 69,173 bp (0.08%) GC percentage = 40.31% >>>>>>> Mismatches and indels general error rate = 0.0084 number of mismatches = 735,605 number of insertions = 6,650 mapped reads with insertion percentage = 0.49% number of deletions = 27,421 mapped reads with deletion percentage = 2% homopolymer indels = 47.14% >>>>>>> Coverage mean coverageData = 0.0288X std coverageData = 0.252X There is a 2.27% of reference with a coverageData >= 1X There is a 0.44% of reference with a coverageData >= 2X There is a 0.1% of reference with a coverageData >= 3X There is a 0.03% 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 7847953 0.03148619236539435 0.3761096630605162 chr2 243199373 6422621 0.026408871539319305 0.27736745720508593 chr3 198022430 5347082 0.027002405737572253 0.20179171230426357 chr4 191154276 1906361 0.0099728922621642 0.1257441282357961 chr5 180915260 8282198 0.0457794328681837 0.2608934138472429 chr6 171115067 6411924 0.03747141682152396 0.27679902272108975 chr7 159138663 1546520 0.009718065810317885 0.16823242233730715 chr8 146364022 3300360 0.022548984066589808 0.23011201455201408 chr9 141213431 2748620 0.01946429585724038 0.20514078009909262 chr10 135534747 5420220 0.03999136841270674 0.29472088384147294 chr11 135006516 2200510 0.01629928736180408 0.1926688429009273 chr12 133851895 2435780 0.018197575760881084 0.16577185559824614 chr13 115169878 2544780 0.022095881702679235 0.18371410412049968 chr14 107349540 5899207 0.05495325829994241 0.2893117100789324 chr15 102531392 3872714 0.03777100773195394 0.2394776223492074 chr16 90354753 2559312 0.028325150753275814 0.21778900931380127 chr17 81195210 1309180 0.016123857552680754 0.15547800187467892 chr18 78077248 3371292 0.04317892966719319 0.43438474272541994 chr19 59128983 1638605 0.027712382606005587 0.26885475217984073 chr20 63025520 2180377 0.034595144950807226 0.22728619240056264 chr21 48129895 1553849 0.032284487634971985 0.22159554298375828 chr22 51304566 420094 0.00818823806052662 0.10711169960866332 chrMT 16571 4722 0.28495564540462254 0.6631907099311835 chrX 155270560 9586174 0.06173851630341257 0.3226096232487113 chrY 59373566 248339 0.004182652596611765 0.08501831850340802