BamQC report ----------------------------------- >>>>>>> Input bam file = SRR1505983.sorted.bam outfile = /mainsd2/zhouyj/SRP013572/SRP013572.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 = 9,218,699 number of mapped reads = 7,286,868 (79.04%) number of supplementary alignments = 257 (0%) number of secondary alignments = 0 number of mapped bases = 342,285,289 bp number of sequenced bases = 342,217,992 bp number of aligned bases = 0 bp number of duplicated reads (estimated) = 366,742 duplication rate = 3.71% >>>>>>> Insert size mean insert size = 0 std insert size = 0 median insert size = 0 >>>>>>> Mapping quality mean mapping quality = 45.9303 >>>>>>> ACTG content number of A's = 104,248,959 bp (30.46%) number of C's = 67,012,497 bp (19.58%) number of T's = 102,802,827 bp (30.04%) number of G's = 68,152,256 bp (19.91%) number of N's = 1,453 bp (0%) GC percentage = 39.5% >>>>>>> Mismatches and indels general error rate = 0.0047 number of mismatches = 1,590,407 number of insertions = 16,545 mapped reads with insertion percentage = 0.23% number of deletions = 49,203 mapped reads with deletion percentage = 0.67% homopolymer indels = 47.59% >>>>>>> Coverage mean coverageData = 0.1106X std coverageData = 0.8742X There is a 8.41% of reference with a coverageData >= 1X There is a 1.84% of reference with a coverageData >= 2X There is a 0.43% of reference with a coverageData >= 3X There is a 0.11% of reference with a coverageData >= 4X There is a 0.03% of reference with a coverageData >= 5X There is a 0.02% of reference with a coverageData >= 6X There is a 0.01% of reference with a coverageData >= 7X There is a 0.01% of reference with a coverageData >= 8X There is a 0.01% of reference with a coverageData >= 9X There is a 0.01% 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 27179285 0.10904400113811552 1.9234657648628652 chr2 243199373 29021721 0.11933304203049898 0.70118765710022 chr3 198022430 24521694 0.12383291125151832 0.4433408980833158 chr4 191154276 23303342 0.1219085572535139 0.4432252391184536 chr5 180915260 21114857 0.11671131003542763 0.4336905199717441 chr6 171115067 20672670 0.120811512173852 0.5857506773445578 chr7 159138663 18431954 0.11582323021024753 1.1302189187054386 chr8 146364022 18214521 0.12444670999817155 1.3286643548265284 chr9 141213431 15225912 0.10782198189066025 0.633473201470297 chr10 135534747 15978144 0.11788965083618004 0.8944288264062049 chr11 135006516 15168431 0.1123533252276505 0.6954789448983492 chr12 133851895 14884194 0.11119897854266464 0.45884089088945884 chr13 115169878 11320297 0.09829216802678215 0.38318837297539693 chr14 107349540 10372295 0.0966216995433795 0.47100103874081056 chr15 102531392 9162743 0.08936524532896227 0.36704376958034224 chr16 90354753 8888060 0.09836848317210274 0.483321011912956 chr17 81195210 8027030 0.09886088107906858 0.48387829821578465 chr18 78077248 9514024 0.12185398747660778 1.4669891431262654 chr19 59128983 5758688 0.09739196765822947 1.2542338669872173 chr20 63025520 6512352 0.10332881029779684 0.41954465563298426 chr21 48129895 4453404 0.09252885342883047 0.4237447053660583 chr22 51304566 3667267 0.07148032399299509 0.3272692099969091 chrMT 16571 21584 1.3025164443908033 1.3766001870087543 chrX 155270560 19982405 0.12869410015652677 0.568554063010081 chrY 59373566 888415 0.014963140330833421 0.20782580668642478