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
A2 F1 I1 R1	748	32.0	1685426	92.6%	1560704	103.9

Breseq alignment

BRESEQ :: Evidence

Predicted mutation
evidence	seq id	position	mutation	annotation	gene	description
RA	NC_000913	2,379,348	C→T	432 (TAG→TAA)	menF ←	isochorismate synthase 2

Read alignment evidence...
	seq id	position		ref	new	freq	score (cons/poly)	reads	annotation	genes	product
*	NC_000913	2,379,348	0	C	T	100.0%	137.3 / NA	43	432 (TAG→TAA)	menF	isochorismate synthase 2
Reads supporting (aligned to +/- strand): ref base C (0/0); new base T (23/20); total (23/20)

CCAGAATGACCGCCGCCCAGCGTCGGTTAAATGCGCTTACTGACATGAGTTTGTCCGGTATCAATATTGCGGCTAAGTATAAGGAGCTACAAAAATAGATTATTGATATGAATCGGTAATGATGCGACTCATTACTATTCCATTTGTAATAAAGTACGCAGCCCTGCCGCTTTGTTGTCGATTTCCTGCCACTCTTGCTCGGGGTCGGAACCACGGACAATGCCCGCGCCAGCATATAATCGCACGACATTGCCGCTAATTTT  >  NC_000913/2379214‑2379476

ccAGAATGACCGCCGCCCAGCGTCGGTTAAATGCGCTTACTGACATGAGTTTGTCCGGTATCAATATTGCGGCTAAGTATAAGGAGCTACAAAAATAGATTATTGATATGAATCGGTAATGATGCGACTCattattatt                                                                                                                              >  2:564447/1‑139 (MQ=255)

         ccgccgCCCAGCGTCGGTTAAATGCGCTTACTGACATGAGTTTGTCCGGTATCAATATTGCGGCTAAGTATAAGGAGCTACAAAAATAGATTATTGATATGAATCGGTAATGATGCGACTCATTATTATTCCATTTGta                                                                                                                     >  1:270069/1‑139 (MQ=255)

          cgccgcCCAGCGTCGGTTAAATGCGCTTACTGACATGAGTTTGTCCGGTATCAATATTGCGGCTAAGTATAAGGAGCTACAAAAATAGATTATTGATATGAATCGGTAATGATGCGACTCATTATTATTCCAt                                                                                                                          <  2:27157/133‑1 (MQ=255)

          cgccgcCCAGCGTCGGTTAAATGCGCTTACTGACATGAGTTTGTCCGGTATCAATATTGCGGCTAAGTATAAGGAGCTACAAAAATAGATTATTGATATGAATCGGTAATGATGCGACTCATTATTATTCCAt                                                                                                                          >  1:27157/1‑133 (MQ=255)

            ccgccCAGCGTCGGTTAAATGCGCTTACTGACATGAGTTTGTCCGGTATCAATATTGCGGCTAAGTATAAGGAGCTACAAAAATAGATTATTGATATGAATCGGTAATGATGCGACTCATTATTATTCCATTTGta                                                                                                                     <  2:94970/136‑1 (MQ=255)

            ccgccCAGCGTCGGTTAAATGCGCTTACTGACATGAGTTTGTCCGGTATCAATATTGCGGCTAAGTATAAGGAGCTACAAAAATAGATTATTGATATGAATCGGTAATGATGCGACTCATTATTATTCCATTTGta                                                                                                                     >  1:94970/1‑136 (MQ=255)

              gccCAGCGTCGGTTAAATGCGCTTACTGACATGAGTTTGTCCGGTATCAATATTGCGGCTAAGTATAAGGAGCTACAAAAATAGATTATTGATATGAATCGGTAATGATGCGACTCATTATTATTCCATTTGTAATaaa                                                                                                                <  2:263970/139‑1 (MQ=255)

                                   cTTACTGACATGAGTTTGTCCGGTATCAATATTGCGGCTAAGTATAAGGAGCTACAAAAATAGATTATTGATATGAATCGGTAATGATGCGACTCATTATTATTCCATTTGTAATAAAGTACGCAGCCCTGCCGCTttg                                                                                           <  1:564447/139‑1 (MQ=255)

                                    ttACTGACATGAGTTTGTCCGGTATCAATATTGCGGCTAAGTATAAGGAGCTACAAAAATAGATTATTGATATGAATCGGTAATGATGCGACTCATTATTATTCCATTTGTAATAAAGTACGCAGCCCTGCCGCTttgt                                                                                          >  2:302398/1‑139 (MQ=255)

                                    ttACTGACATGAGTTTGTCCGGTATCAATATTGCGGCTAAGTATAAGGAGCTACAAAAATAGATTATTGATATGAATCGGTAATGATGCGACTCATTATTATTCCATTTGTAATAAAGTACGCAGCCCTGCCGCTttgt                                                                                          >  1:140750/1‑139 (MQ=255)

                                        tGACATGAGTTTGTCCGGTATCAATATTGCGGCTAAGTATAAGGAGCTACAAAAATAGATTATTGATATGAATCGGTAATGATGCGACTCATTATTATTCCATTTGTAATAAAGTACg                                                                                                           <  2:477217/118‑1 (MQ=255)

                                        tGACATGAGTTTGTCCGGTATCAATATTGCGGCTAAGTATAAGGAGCTACAAAAATAGATTATTGATATGAATCGGTAATGATGCGACTCATTATTATTCCATTTGTAATAAAGTACg                                                                                                           >  1:477217/1‑118 (MQ=255)

                                          aCATGAGTTTGTCCGGTATCAATATTGCGGCTAAGTATAAGGAGCTACAAAAATAGATTATTGATATGAATCGGTAATGATGCGACTCATTATTATTCCATTTGTAATAAAGTACGCAGCCCTGCCGCTTTGTTGTCGa                                                                                    <  2:270069/139‑1 (MQ=255)

                                             tGAGTTTGTCCGGTATCAATATTGCGGCTAAGTATAAGGAGCTACAAAAATAGATTATTGATATGAATCGGTAATGATGCGACTCATTATTATTCCATTTGTAATAAAGTACGCAGCCCTGCCGCTTTGTTGTCGAttt                                                                                 <  1:302398/139‑1 (MQ=255)

                                                 tttGTCCGGTATCAATATTGCGGCTAAGTATAAGGAGCTACAAAAATAGATTATTGATATGAATCGGTAATGATGCGACTCattattatt                                                                                                                              <  1:192024/90‑1 (MQ=255)

                                                 tttGTCCGGTATCAATATTGCGGCTAAGTATAAGGAGCTACAAAAATAGATTATTGATATGAATCGGTAATGATGCGACTCattattatt                                                                                                                              >  2:192024/1‑90 (MQ=255)

                                                  ttGTCCGGTATCAATATTGCGGCTAAGTATAAGGAGCTACAAAAATAGATTATTGATATGAATCGTTAATGATGCGACTCATTATTATTCCATTTGTAATAAAGTACGCAGCCCTGCCGCTTTGTTGTCGATTTCCTGc                                                                            <  2:329855/139‑1 (MQ=255)

                                                                    gCGGCTAAGTATAAGGAGCTACAAAAATAGATTATTGATATGAATCGGTAATGATGCGACTCATTATTATTCCATTTGTAATAAAGTACGCAGCCCTGCCGCTTTGTTGTCGATTTCCTGCCACTCTTGCTCGGGGTCg                                                          >  1:348710/1‑139 (MQ=255)

                                                                     cGGCTAAGTATAAGGAGCTACAAAAATAGATTATTGATATGAATCGGTAATGATGCGACTCATTATTATTCCATTTGTAATAAAGTACGCAGCCCTGCCGCTTTGTTGTCGATTTCCTGCCACTCTTGCTc                                                                 <  2:779994/131‑1 (MQ=255)

                                                                     cGGCTAAGTATAAGGAGCTACAAAAATAGATTATTGATATGAATCGGTAATGATGCGACTCATTATTATTCCATTTGTAATAAAGTACGCAGCCCTGCCGCTTTGTTGTCGATTTCCTGCCACTCTTGCTc                                                                 >  1:779994/1‑131 (MQ=255)

                                                                        cTAAGTATAAGGAGCTACAAAAATAGATTATTGATATGAATCGGTAATGATGCGACTCATTATTATTCCATTTGTAATaaa                                                                                                                >  1:575860/1‑81 (MQ=255)

                                                                        cTAAGTATAAGGAGCTACAAAAATAGATTATTGATATGAATCGGTAATGATGCGACTCATTATTATTCCATTTGTAATaaa                                                                                                                <  2:575860/81‑1 (MQ=255)

                                                                                     gCTACAAAAATAGATTATTGATATGAATCGGTAATGATGCGACTCATTATTATTCCATTTGTAATAAAGTACGCAGCCCTGCCGCTTTGTTGTCGATTTCCTGCCACTCTTGCTCGGGGTCGGAACCACGGACAATGcc                                         >  2:54913/1‑139 (MQ=255)

                                                                                      cTACAAAAATAGATTATTGATATGAATCGGTAATGATGCGACTCATTATTATTCCATTTGTAATAAAGTACGCAGCCCTGCCGCTTTGTTGTCGATTTCCTGCCACTCTTGCTc                                                                 >  2:425222/1‑114 (MQ=255)

                                                                                      cTACAAAAATAGATTATTGATATGAATCGGTAATGATGCGACTCATTATTATTCCATTTGTAATAAAGTACGCAGCCCTGCCGCTTTGTTGTCGATTTCCTGCCACTCTTGCTc                                                                 <  1:425222/114‑1 (MQ=255)

                                                                                      cTACAAAAATAGATTATTGATATGAATCGGTAATGATGCGACTCATTATTATTCCATTTGTAATAAAGTACGCAGCCCTGCCGCTTTGTTGTCGATTTCCTGCCACTCTTGCTCGGGGTCGGAACCACGGACAATGccc                                        >  1:599270/1‑139 (MQ=255)

                                                                                      cTACAAAAATAGATTATTGATATGAATCGGTAATGATGCGACTCATTATTATTCCATTTGTAATAAAGTACGCAGCCCTGCCGCTTTGTTGTCGATTTCCTGCCACTCTTGCTCGGGGTCGGAACCACGGACAATGccc                                        >  1:193546/1‑139 (MQ=255)

                                                                                      cTACAAAAATAGATTATTGATATGAATCGGTAATGATGCGACTCATTATTATTCCATTTGTAATAAAGTACGCAGCCCTGCCGCTTTGTTGTCGATTTCCTGCCACTCTTGCTCGGGGTCGGAACCACGGACAATGccc                                        >  1:565737/1‑139 (MQ=255)

                                                                                       tACAAAAATAGATTATTGATATGAATCGGTAATGATGCGACTCATTATTATTCCATTTGTAATAAAGTACGCAGCCCTGCCGCTTTGTTGTCGATTTCCTGCCACTCTTGCTCGGGGTCGGAACCACGGACAATGCCcg                                       <  1:288688/139‑1 (MQ=255)

                                                                                       tACAAAAATAGATTATTGATATGAATCGGTAATGATGCGACTCATTATTATTCCATTTGTAATAAAGTACGCAGCCCTGCCGCTTTGTTGTCGATTTCCTGCCACTCTTGCTCGGGGTCGGAACCACGGACAATGCCcg                                       >  1:52136/1‑139 (MQ=255)

                                                                                          aaaaaTAGATTATTGATATGAATCGGTAATGATGCGACTCATTATTATTCCATTTGTAATAAAGTACGCAGCCCTGCCGCTTTGTTGTCGATTTCCTGCCACTCTTGCTCGGGGTCGGAACCACGGACAATGCCCgcgc                                    <  1:226458/139‑1 (MQ=255)

                                                                                          aaaaaTAGATTATTGATATGAATCGGTAATGATGCGACTCAGTATTATTCCATTTGTAATAAAGTACGCAGCCCTGCCGCTTTGTTGTCGATTTCCTGCCACTCTTGCTCGGGGTCGGAACCACGGACAATGCCCgcgc                                    <  2:193546/139‑1 (MQ=255)

                                                                                                      ttGATATGAATCGGTAATGATGCGACTCATTATTATTCCATTTGTAATAAAGTACGCAGCCCTGCCGCTTTGTTGTCGAtt                                                                                  >  1:107495/1‑81 (MQ=255)

                                                                                                      ttGATATGAATCGGTAATGATGCGACTCATTATTATTCCATTTGTAATAAAGTACGCAGCCCTGCCGCTTTGTTGTCGAtt                                                                                  <  2:107495/81‑1 (MQ=255)

                                                                                                      ttGATATGAATCGGTAATGATGCGACTCATTATTATTCCATTTGTAATAAAGTACGCAGCCCTGCCGCTTTGTTGTCGATTTCCTGCCACTCTTGCTCGGGGTCGGAACCACGGACAATGCCCGCGCCAGCATATAATc                        >  2:842293/1‑139 (MQ=255)

                                                                                                                          tgCGACTCATTATTATTCCATTTGTAATAAAGTACGCAGCCCTGCCGCTTTGTTGTCGAtt                                                                                  <  2:234327/61‑1 (MQ=255)

                                                                                                                          tgCGACTCATTATTATTCCATTTGTAATAAAGTACGCAGCCCTGCCGCTTTGTTGTCGAtt                                                                                  >  1:234327/1‑61 (MQ=255)

                                                                                                                           gCGACTCATTATTATTCCATTTGTAATAAAGTACGCAGCCCTGCCGCTTTGTTGTCGATTTCCTGCCACTCTTGCTCGGGGTCGGAACCACGGACAATGCCcg                                       >  2:286566/1‑103 (MQ=255)

                                                                                                                           gCGACTCATTATTATTCCATTTGTAATAAAGTACGCAGCCCTGCCGCTTTGTTGTCGATTTCCTGCCACTCTTGCTCGGGGTCGGAACCACGGACAATGCCcg                                       <  1:286566/103‑1 (MQ=255)

                                                                                                                            cGACTCATTATTATTCCATTTGTAATAAAGTACGCAGCCCTGCCGCTTTGTTGTCGATTTCCTGCCACTCTTGCTCGGGGTCGGAACCACGGACAATGCCCGCGCCAGCATATAATCGCACGACATTGCCGCTAAtttt  >  1:714408/1‑139 (MQ=255)

                                                                                                                             gACTCATTATTATTCCATTTGTAATAAAGTACGCAGCCCTGCCGCTTTGTTGTCGATTTCCTGCCACTCTTGCTCg                                                                >  1:261187/1‑76 (MQ=255)

                                                                                                                             gACTCATTATTATTCCATTTGTAATAAAGTACGCAGCCCTGCCGCTTTGTTGTCGATTTCCTGCCACTCTTGCTCg                                                                <  2:261187/76‑1 (MQ=255)

                                                                                                                              aCTCATTATTATTCCATTTGTAATAAAGTACGCAGCCCTGCCGCTTTGTTGTCGATTTCCTGCCACTCTTGCTCGGGGTCGGAACCACGGACa                                              >  2:114239/1‑93 (MQ=255)

                                                                                                                              aCTCATTATTATTCCATTTGTAATAAAGTACGCAGCCCTGCCGCTTTGTTGTCGATTTCCTGCCACTCTTGCTCGGGGTCGGAACCACGGACa                                              <  1:114239/93‑1 (MQ=255)

                                                                                                                              aCTCATTATTATTCCATTTGTAATAAAGTACGCAGCCCTGCCGCTTTGTTGTCGATTTCCTGCCACTCTTGCTCGGGGTCGGAACCACGGACAATGCCCGCGCCAGCATATAATCGCACGACATTGCCGCt        <  2:372812/131‑1 (MQ=255)

                                                                                                                              aCTCATTATTATTCCATTTGTAATAAAGTACGCAGCCATGCCGCTTTGTTGTCGATTTCCTGCCACTCTTGCTCGGGGTCGGAACCACGGACAATGCCCGCGCCAGCATATAATCGCACGACATTGCCGCt        >  1:372812/1‑131 (MQ=255)

                                                                                                                                   ttattaTTCCATTTGTAATAAAGTACGCAGCCCTGCCGCTTTGTTGTCGATTTCCTGCCACTCTTGCTCGGGGTCGGAACCa                                                    >  1:188946/1‑82 (MQ=255)

                                                                                                                                   ttattaTTCCATTTGTAATAAAGTACGCAGCCCTGCCGCTTTGTTGTCGATTTCCTGCCACTCTTGCTCGGGGTCGGAACCACGGACAATGCCCgcgc                                    <  2:2349/98‑1 (MQ=255)

CCAGAATGACCGCCGCCCAGCGTCGGTTAAATGCGCTTACTGACATGAGTTTGTCCGGTATCAATATTGCGGCTAAGTATAAGGAGCTACAAAAATAGATTATTGATATGAATCGGTAATGATGCGACTCATTACTATTCCATTTGTAATAAAGTACGCAGCCCTGCCGCTTTGTTGTCGATTTCCTGCCACTCTTGCTCGGGGTCGGAACCACGGACAATGCCCGCGCCAGCATATAATCGCACGACATTGCCGCTAATTTT  >  NC_000913/2379214‑2379476

Alignment Legend
Aligned base mismatch/match (shaded by quality score): `ATCG/ATCG` `< 3 ≤` `ATCG/ATCG` `< 16 ≤` `ATCG/ATCG` `< 34 ≤` `ATCG/ATCG` `< 38 ≤` `ATCG/ATCG` `< 40 ≤` `ATCG/ATCG`
Unaligned base: `atcg` Masked matching base: `atcg` Alignment gap: `‑` Deleted base: `‑`

GATK/CNVnator alignment

N/A