Sample Resequencing Stats

Note: The mutation counts shown below represent unfiltered mutation sets.

ALE, Flask, Isolate	Predicted Mutations	Mean Coverage	Total Reads	Percent Mapped	Mapped Reads	Average Read Length
A23 F60 I1 R1	18	61.6	2092650	99.2%	2075908	139.4

Breseq alignment

BRESEQ :: Evidence

Predicted mutation
evidence	seq id	position	mutation	annotation	gene	description
RA	NC_000913	3,815,883	+C	coding (667/687 nt)	rph ←	truncated RNase PH

Read alignment evidence...
	seq id	position		ref	new	freq	score (cons/poly)	reads	annotation	genes	product
*	NC_000913	3,815,879	1	.	C	94.7%	132.5 / 0.1	38	coding (671/687 nt)	rph	truncated RNase PH
Reads supporting (aligned to +/- strand): ref base . (1/1); new base C (14/22); total (15/23)
Fisher's exact test for biased strand distribution p-value = 1.00e+00
Kolmogorov-Smirnov test that lower quality scores support variant p-value = 9.97e-01

ACTGGCGCTGATATGGTTTCATGCCTTCGCTCCTCATCTTACTTTTCTACAGACAAAAAAAAGGCGACTCATCAGTCGCCTTAAAAATCAGTTTGCCAGCGCCGCCTTCTGCGTCGCTACAATGGATTCG‑A‑TT‑C‑CCCTCGGGCCAGAGCCAACAAGATGAGTAGCTCTTCATGGGTGAACGGCTCGCCTTCTGCCGTCCCCTGCACTTCAATGATGCGCCCGTCTTCGGTCATCACTACGTTCATGTCGGTCTCTGCGGCAGAGTC  >  NC_000913/3815747‑3816012

aCTGGCGCTGATATGGTTTCATGCCTTCGCTCCTCATCTTACTTTTCTACAGACAAAAAAAAGGCGACTCATCAGTCGCCTTAAAAATCAGTTTGCCAGCGCCGCCTTCTGCGTCGCTACAATGGATTCG‑A‑TT‑c‑cccctc                                                                                                                                >  1:225138/1‑137 (MQ=255)

   ggCGCTGATATGGTTTCATGCCTTCGCTCCTCATCTTACTTTTCTACAGACAAAAAAAAGGCGACTCATCAGTCGCCTTAAAAATCAGTTTGCCAGCGCCGCCTTCTGCGTCGCTACAATGGATTCG‑A‑TTCC‑CCCTCggg                                                                                                                              >  2:663584/1‑140 (MQ=255)

     cgcTGATATGGTTTCATGCCTTCGCTCCTCATCTTACTTTTCTACAGACAAAAAAAAGGCGACTCATCAGTCGCCTTAAAAATCAGTTTGCCAGCGCCGCCTTCTGCGTCGCTACAATGGATTCG‑A‑TTCC‑CCCTCGGGcc                                                                                                                            >  1:146950/1‑140 (MQ=255)

       cTGATATGGTTTCATGCCTTCGCTCCTCATCTTACTTTTCTACAGACAAAAAAAAGGCGACTCATCAGTCGCCTTAAAAATCAGTTTGCCAGCGCCGCCTTCTGCGTCGCTACAATGGATTCG‑A‑TTCC‑CCCTCGGGCCag                                                                                                                          >  2:827441/1‑140 (MQ=255)

         gATATGGTTTCATGCCTTCGCTCCTCATCTTACTTTTCTACAGACAAAAAAAAGGCGACTCATCAGTCGCCTTAAAAATCAGTTTGCCAGCGCCGCCTTCTGCGTCGCTACAATGGATTCG‑A‑TTCC‑CCCTCGGGCCagag                                                                                                                        <  1:544816/140‑1 (MQ=255)

           tatGGTTTCATGCCTTCGCTCCCCATCTTCCTTTTCTCCAGACAAAAAAAAGGCGACTCATCAGTCGCCTTAAAAATCAGTTTGCCAGCGCCGCCTTCTGCGTCGCTACAATGGATTCG‑A‑TTCC‑CCCTCGGGCCAGAGcc                                                                                                                      <  1:306828/140‑1 (MQ=255)

            atGGTTTCATGCCTTCGCTCCTCATCTTACTTTTCTACAGACAAAAAAAAGGCGACTCATCAGTCGCCTTAAAAATCAGTTTGCCAGCGCCGCCTTCTGCGTCGCTACAATGGATTCG‑A‑TTCC‑CCCTCGGGCCAGAGCca                                                                                                                     >  2:225418/1‑140 (MQ=255)

            atGGTTTCATGCCTTCGCTCCTCATCTTACTTTTCTACAGACAAAAAAAAGGCGACTCATCAGTCGCCTTAAAAATCAGTTTGCCAGCGCCGCCTTCTGCGTCGCTACAATGGATTCG‑A‑TTCC‑CCCTCGGGCCAGAGCca                                                                                                                     <  1:749068/140‑1 (MQ=255)

              ggTTTCATGCCTTCGCTCCTCATCTTACTTTTCTACAGACAAAAAAAAGGCGACTCATCAGTCGCCTTAAAAATCAGTTTGCCAGCGCCGCCTCCTGCGTCGCTACAATGGATTCG‑A‑TTCC‑CCCTCGGGCCAGAGCcaac                                                                                                                   <  2:635842/140‑1 (MQ=255)

              ggTTTCATGCCTTCGCTCCTCATCTGACTCTTCTACACACAAAAAAAAGGCGACTCATCAGTCGCCTTAAAAATCAGTTTGCCAGCGCCGCCTTCTGCGTCGCTACAATGGATTCG‑A‑TTCC‑CCCTCGGGCCAGAGCcaac                                                                                                                   <  1:403867/140‑1 (MQ=255)

                    aTGCCTTCGCTCCTCATCTTACTTTTCTACAGACAAAAAAAAGGCGACTCATCAGTCGCCTTAAAAATCAGTTTGCCAGCGCCGCCTTCTGCGTCGCTACAATGGATTCG‑A‑TTCC‑CCCTCGGGCCAGAGcc                                                                                                                      >  1:163551/1‑131 (MQ=255)

                    aTGCCTTCGCTCCTCATCTTACTTTTCTACAGACAAAAAAAAGGCGACTCATCAGTCGCCTTAAAAATCAGTTTGCCAGCGCCGCCTTCTGCGTCGCTACAATGGATTCG‑A‑TTCC‑CCCTCGGGCCAGAGcc                                                                                                                      <  2:163551/131‑1 (MQ=255)

                    aTGCCTTCGCTCCTCATCTTACTTTTCTACAGACAAAAAAAAGGCGACTCATCAGTCGCCTTAAAAATCAGTTTGCCAGCGCCGCCTTCTGCGTCGCTACAATGGATTCG‑A‑TTCC‑CCCTCGGGCCAGAGCGAACAAGATg                                                                                                             >  2:607036/1‑140 (MQ=255)

                    aTGCCTTCGCTCCTCATCTTACTTTTCTACAGACAAAAAAAAGGCGACTCATCAGTCGCCTTAAAAATCAGTTTGCCAGCGCCGCCTTCTGCGTCGCTACAATGGATTCG‑A‑TTCC‑CCCTCGGGCCAGAGCCAACAAGATg                                                                                                             >  1:813316/1‑140 (MQ=255)

                    aTGCCTTCGCTCCTCATCTTACTTTTCTACAGACAAAAAAAAGGCGACTCATCAGTCGCCTTAAAAATCAGTTTGCCAGCGCCGCCTTCTGCGTCGCTACAATGGATTCG‑A‑TTCC‑CCCTCGGGCCAGAGCCAACAAGATg                                                                                                             >  2:81939/1‑140 (MQ=255)

                     tGCCTTCGCTCCTCATCTTACTTTTCTACAGACAAAAAAAAGGCGACTCATCAGTCGCCTTAAAAATCAGTTTGCCAGCGCCGCCTTCTGCGTCGCTACAATGGATTCG‑A‑TTCC‑CCCTCGGGCCAGAGCCAACAAGATGa                                                                                                            >  1:1013909/1‑140 (MQ=255)

                      gCCTTCGCTCCTCATCTTACTTTTCTACAGACAAAAAAAAGGCGACTCATCAGTCGCCTTAAAAATCAGTTTGCCAGCGCCGCCTTCTGCGTCGCTACAATGGATTCG‑A‑TTCC‑CCCTCGGGCCAGAGCCAACAAGATGAg                                                                                                           <  2:813316/140‑1 (MQ=255)

                         ttCGCTCCTCATCTTACTTTTCTACAGACAAAAAAAAGGCGACTCATCAGTCGCCTTAAAAATCAGTTTGCCAGCGCCGCCTTCTGCGTCGCTACAATGGATTCG‑A‑TTCC‑CCCTCGGGCCAGAGCCAACAAGATGAGTAg                                                                                                        <  2:146950/140‑1 (MQ=255)

                         ttCGCTCCTCATCTTACTTTTCTACAGACAAAAAAAAGGCGACTCATCAGTCGCCTTAAAAATCAGTTTGCCAGCGCCGCCTTCTGCGTCGCTACAATGGATTCG‑A‑TTCC‑CCCTCGGGCCAGAGCCAACAAGATGAGTAg                                                                                                        <  1:225418/140‑1 (MQ=255)

                         ttCGCTCCCCATCTTATATTTCCACAGACAAAAAATAGGGGACTCATCGGTCGCCTTAAAAATCAGTTTGCCAGCGCCGCCTTCTGCGTCGCTACAATGGATTCG‑A‑TTCC‑CCCTCGGGCCAGAGCCAACAAGATGAGTAg                                                                                                        <  2:499567/140‑1 (MQ=255)

                          tCGCTCCTCATCTTACTTTTCTACAGACAAAAAAAAGGCGACTCATCAGTCGCCTTAAAAATCAGTTTGCCAGCGCCGCCTTCTGCGTCGCTACAATGGATTCG‑A‑TTCC‑CCCTCGGGCCAGAGCCAACAAGATGAGTAGc                                                                                                       >  2:105860/1‑140 (MQ=255)

                                  cATCTTACTTTTCTACAGACAAAAAAAAGGCGACTCATCAGTCGCATTAAAAATCAGTTTGCCAGCGCCGCCTTCTGCGTCGCTACAATGGATTCG‑A‑TTCC‑CCCTCGGGCCAGAGCCAACAAGATGAGTAGCTCTTCATg                                                                                               >  2:849487/1‑140 (MQ=255)

                                        aCTTTTCTACAGACAAAAAAAAGGCGACTCATCAGTCGCCTTAAAAATCAGTTTGCCAGCGCCGCCTTCTGCGTCGCTACAATGGATTCGAA‑TC‑C‑CCCTCGGGCGAAACCCAACAAGCTGAGGAGCTCTTCATGGGTGaa                                                                                         >  2:498457/1‑140 (MQ=255)

                                            ttCTACAGACAAAAACAAGGCGCCTTATCCGTCGCCTTAAAAATCAGTTTGCCAGCGCCGCCTTCTGCGTCGCTACAATGGATTCG‑A‑TTCC‑CCCTCGGGCCAGAGCCAACAAGATGAGTAGCTCTTCATGGGTGAACGGc                                                                                     <  1:498457/140‑1 (MQ=255)

                                               tACAGACAAAAAAAAGGCGACTCATCAGTCGCCTTAAAAATCAGTTTGCCAGCGCCGCCTTCTGCGTCGCTACAATGGATTCG‑A‑TTCC‑CCCTCGGGCCAGAGCCAACAAGATGAGTAGCTCTTCATGGGTGAACGGCTCg                                                                                  >  1:230241/1‑140 (MQ=255)

                                                           aaaGGCGACTCATCAGTCGCCTTAAAAATCAGTTTGCCAGCGCCGCCTTCTGCGTCGCTACAATGGATTCG‑A‑TTCC‑CCCTCGGGCCAGAGCCAACAAGATGAGTAGCTCTTCATGGGTGAACGGCTCGCCTTCTGCCGTc                                                                      <  1:827441/140‑1 (MQ=255)

                                                             aGGCGACTCATCAGTCGCCTTAAAAATCAGTTTGCCAGCGCCGCCTTCTGCGTCGCTACAATGGATTCG‑A‑TTCC‑CCCTCGGGCCAGAGCCAACAAGATGAGTAGCTCTTCATGGGTGAACGGCTCGCCTTCTGCCGTccc                                                                    <  1:81939/140‑1 (MQ=255)

                                                                cGACTCATCAGTCGCCTTAAAAATCAGTTTGCCAGCGCCGCCTTCTGCGTCGCTACAATGGATTCG‑A‑TTCC‑CCCTCGGGCCAGAGCCAACAAGATGAGTAGCTCTTCATGGGTGAACGGCTCGCCTTCTGCCGTCCCCTg                                                                 <  2:973630/140‑1 (MQ=255)

                                                                                ttAAAAATCAGTTTGCCAGCGCCGCCTTCTGCGTCGCTACAATGGATTCG‑A‑TTCC‑CCCTCGGGCCAGAGCCAACAAGATGAGTAGCTCTTCATGGGTGAACGGCTCGCCTTCTGCCGTCCCCTGCACTTCAATGATgcgc                                                 <  1:105860/140‑1 (MQ=255)

                                                                                ttAAAAATCAGTTTGCCAGCGCCGCCTTCTGCGTCGCTACAATGGATTCG‑A‑TTCC‑CCCTCGGGCCAGAGCCAACAAGATGAGTAGCTCTTCATGGGTGAACGGCTCGCCTTCTGCCGTCCCCTGCACTTCAATGATgcgc                                                 <  2:230241/140‑1 (MQ=255)

                                                                                         aGTTTGCCAGCGCCGCCTTCTGCGTCGCTACAATGGATTCG‑A‑TTCC‑CCCTCGGGCCAGAGCCAACAAGATGAGTAGCTCTTCATGGGTGAAGGGCTCGCCTTCTCCGGTCCCCTGCAATTCAATGATGCGCCCGTCTTCg                                        >  2:494297/1‑140 (MQ=255)

                                                                                         aGTTTGCCAGCGCCGCCTTCTGCGTCGCTACAATGGATTCG‑A‑TTCC‑CCCTCGGGCCAGAGCCAACAAGATGAGTAGCTCTTCATGGGTGAACGGCTCGCCTTCTGCCGTCCCCTGCACTTCAATGATGCGCCCGTCTTCg                                        <  1:663584/140‑1 (MQ=255)

                                                                                             tGCCAGCGCCGCCTTCTGCGTCGCTGCAAGGGATTCG‑A‑TTCC‑CCCTCGGGCCAGAGCCAACAAGATGAGTAGCTCTTCATGGGTGAACGGCTCGCCTTCTGCCGTCCCCTGCACTTCAATGATGCGCCCGTCTTCGGtca                                    <  1:368067/140‑1 (MQ=255)

                                                                                              gCCAGCGCCGCCTTCTGCGTCGCTACAATGGATTCG‑A‑TTCC‑CCCTCGGGCCAGAGCCAACAAGATGAGTAGCTCTTCATGGGTGAACGGCTCGCCTTCTGCCGTCCCCTGCACTTCAATGATGCGCCCGTCTTCGGtcat                                   <  1:53439/140‑1 (MQ=255)

                                                                                                cAGCGCCGCCTTCTGCCACGCTTCAATGGAAACC‑ACTC‑C‑CCCTCGGGCCAGAGCCAACAAGATGAGTAGCTCTTCATGGGTGAACGGCTCGCCTTCTGCCGTCCCCTGCACTTCAATGATGCGCCCGTCTTCGGtcatca                                 <  2:493712/140‑1 (MQ=255)

                                                                                                  gctccgccTTCTGCGTCGCTACAATGGATTCG‑A‑TTCC‑CCCTCGGGCCAGAGCCAACAAGATGAGTAGCTCTTCATGGGTGAACGGCTCGCCTTCTGCCGTCCCCTGCACTTCAATGATGCGCCCGTCTTCGGTCATCACt                               >  1:185556/4‑140 (MQ=255)

                                                                                                  gcgcCGCCTTCTGCGTCGCTACAATGGATTCG‑A‑TTCC‑CCCTCGGGCCAGAGCCAACAAGATGAGTAGCTCTTCATGGGTGAACGGCTCGCCTTCTGCCGTCCCCTGCACTTCAATGATGCGCCCGTCTTCGGTCATCACt                               <  1:849487/140‑1 (MQ=255)

                                                                                                       gccTTCTGCGTCGCTACAATGGGTTCG‑A‑TT‑CTCCCACGGGCCAGAGCCTACAAGATGAGTAGCTCTTCATGGGTGAACGGCTCGCCTTCTGCCGTCCCCTGCACTTCAATGATGCGCCCGTCTTCGGTCATCACTACGtt                          <  2:399484/140‑1 (MQ=255)

                                                                                                        ccTTCTGCGTCGCTACAATGGATTCG‑A‑TTCC‑CCCTCGGGCCAGAGCCAACAAGATGAGTAGCTCTTCATGGGTGAACGGCTCGCCTTCTGCCGTCCCCTGCACTTCAATGATGCGCCCGTCTTCGGTCATCACTACGTTc                         <  2:185556/140‑1 (MQ=255)

                                                                                                                          tGGATTCG‑A‑TTCC‑CCCTCGGGCCAGAGCCAACAAGATGAGTAGCTCTTCATGGGTGAACGGCTCGCCTTCTGCCGTCCCCTGCACTTCAATGATGCGCCCGTCTTCGGTCATCACTACGTTCATGTCGGTCTCTGCGGCa       <  2:1013909/140‑1 (MQ=255)

                                                                                                                               tcg‑a‑ttcC‑CCCTCGGGCCAGAGCCAACAAGATGAGTAGCTCTTCATGGGTGAACGGCTCGCCTTCTGCCGTCCCCTGCACTTCAATCATGCGCCCGTCTTTGGTTATCACTACGTTCATGTCCGTCTCTGCGGCAGAGTc  >  2:330078/1‑140 (MQ=255)

ACTGGCGCTGATATGGTTTCATGCCTTCGCTCCTCATCTTACTTTTCTACAGACAAAAAAAAGGCGACTCATCAGTCGCCTTAAAAATCAGTTTGCCAGCGCCGCCTTCTGCGTCGCTACAATGGATTCG‑A‑TT‑C‑CCCTCGGGCCAGAGCCAACAAGATGAGTAGCTCTTCATGGGTGAACGGCTCGCCTTCTGCCGTCCCCTGCACTTCAATGATGCGCCCGTCTTCGGTCATCACTACGTTCATGTCGGTCTCTGCGGCAGAGTC  >  NC_000913/3815747‑3816012

Alignment Legend
Aligned base mismatch/match (shaded by quality score): `ATCG/ATCG` `< 3 ≤` `ATCG/ATCG` `< 15 ≤` `ATCG/ATCG` `< 27 ≤` `ATCG/ATCG` `< 33 ≤` `ATCG/ATCG` `< 40 ≤` `ATCG/ATCG`
Unaligned base: `atcg` Masked matching base: `atcg` Alignment gap: `‑` Deleted base: `‑`

GATK/CNVnator alignment

N/A