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
A16 F60 I1 R1	14	59.5	2012980	98.7%	1986811	139.0

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	100.0%	153.4 / NA	42	E224G (GAA→GGA)	rph	truncated RNase PH
Reads supporting (aligned to +/- strand): ref base . (0/0); new base C (17/25); total (17/25)

AACTGGCGCTGATATGGTTTCATGCCTTCGCTCCTCATCTTACTTTTCTACAGACAAAAAAAAGGCGACTCATCAGTCGCCTTAAAAATCAGTTTGCCAGCGCCGCCTTCTGCGTCGCTACAATGGATTCGATT‑‑CCCCTCGGGCCAGAGCCAACAAGATGAGTAGCTCTTCATGGGTGAACGGCTCGCCTTCTGCCGTCCCCTGCACTTCAATGATGCGCCCGTCTTCGGTCATCACTACGTTCATGTCGGTCTCTGCGGCAGAGTC  >  NC_000913/3815746‑3816012

aaCTGGCGCTGATATGGTTTCATGCCTTCGCTCCTCATCTTACTTTTCTACAGACAAAAAAAAGGCGACTCATCAGTCGCCTTAAAAATCAGTTTGCCAGCGCCGCCTTCTGCGTCGCTACAATGGATTCGATT‑‑ccccct                                                                                                                                 <  1:999721/140‑3 (MQ=255)

     gcgcTGATATGGTTTCATGCCTTCGCTCCTCATCTTACTTTTCTACAGACAAAAAAAAGGCGACTCATCAGTCGCCTTAAAAATCAGTTTGCCAGCGCCGCCTTCTGCGTCGCTACAATGGATTCGATTC‑CCCCTCGGGc                                                                                                                             <  2:28381/140‑1 (MQ=255)

     gcgcTGATATGGTTTCATGCCTTCGCTCCTCATCTTACTTTTCTACAGACAAAAAAAAGGCGACTCATCAGTCGCCTTAAAAATCAGTTTGCCAGCGCCGCCTTCTGCGTCGCTACAATGGATTCGATTC‑CCCCTCGGGc                                                                                                                             <  2:875736/140‑1 (MQ=255)

        cTGATATGGTTTCATGCCTTCGCTCCTCATCTTACTTTTCTACAGACAAAAAAAAGGCGACTCATCAGTCGCCTTAAAAATCAGTTTGCCAGCGCCGCCTTCTGCGTCGCTACAATGGATTCGATTC‑CCCCTCGGGc                                                                                                                             >  2:930713/1‑137 (MQ=255)

        cTGATATGGTTTCATGCCTTCGCTCCTCATCTTACTTTTCTACAGACAAAAAAAAGGCGACTCATCAGTCGCCTTAAAAATCAGTTTGCCAGCGCCGCCTTCTGCGTCGCTACAATGGATTCGATTC‑CCCCTCGGGc                                                                                                                             <  1:930713/137‑1 (MQ=255)

        cTGATATGGTTTCATGCCTTCGCTCCTCATCTTACTTTTCTACAGACAAAAAAAAGGCGACTCATCAGTCGCCTTAAAAATCAGTTTGCCAGCGCCGCCTTCTGCGTCGCTACAATGGATTCGATTC‑CCCCTCGGGCCag                                                                                                                          <  1:548341/140‑1 (MQ=255)

              tGGTTTCATGCCTTCGCTCCTCATCTTACTTTTCTACAGACAAAAAAAAGGCGACTCATCAGTCGCCTTAAAAATCAGTTTGCCAGCGCCGCCTTCTGCGTCGCTACAATGGATTCGATTC‑CCCCTCGGGCCAGAGCcaa                                                                                                                    <  1:557099/140‑1 (MQ=255)

                     aTGCCTTCGCTCCTCATCTTACTTTTCTACAGACAAAAAAAAGGCGACTCATCAGTCGCCTTAAAAATCAGTTTGCCAGCGCCGCCTTCTGCGTCGCTACAATGGATTCGATTC‑CCCCTCGGGCCAGAGCCAACAAGATg                                                                                                             >  2:555869/1‑140 (MQ=255)

                          ttCGCTCCTCATCTTACTTTTCTACAGACAAAAAAAAGGCGACTCATCAGTCGCCTTAAAAATCAGTTTGCCAGCGCCGCCTTCTGCGTCGCTACAATGGATTCGATTC‑CCCCTCGGGCCAGAGCCAACAAGATGAGTAg                                                                                                        <  2:748195/140‑1 (MQ=255)

                          ttCGCTCCTCATCTTACTTTTCTACAGACAAAAAAAAGGCGACTCATCAGTCGCCTTAAAAATCAGTTTGCCAGCGCCGCCTTCTGCGTCGCTACAATGGATTCGATTC‑CCCCTCGGGCCAGAGCCAACAAGATGAGTAg                                                                                                        <  2:752909/140‑1 (MQ=255)

                           tCGCTCCTCATCTTACTTTTCTACAGACAAAAAAAAGGCGACTCATCAGTCGCCTTAAAAATCAGTTTGCCAGCGCCGCCTTCTGCGTCGCTACAATGGATTCGATTC‑CCCCTCGGGCCAGAGcc                                                                                                                      >  2:16014/1‑125 (MQ=255)

                           tCGCTCCTCATCTTACTTTTCTACAGACAAAAAAAAGGCGACTCATCAGTCGCCTTAAAAATCAGTTTGCCAGCGCCGCCTTCTGCGTCGCTACAATGGATTCGATTC‑CCCCTCGGGCCAGAGcc                                                                                                                      <  1:16014/125‑1 (MQ=255)

                               ttctcATCTTACTTTTCTACAGACAAAAAAAAGGCGACTCATCAGTCGCCTTAAAAATCAGTTTGCCAGCGCCGCCTTCTGCGTCGCTACAATGGATTCGATTC‑CCCCTCGGGCCAGCGCCAACAAGATGAGTAGCTCtt                                                                                                   >  1:368181/3‑140 (MQ=255)

                                   cATCTTACTTTTCTACAGACAAAAAAAAGGCGACTCATCAGTCGCCTTAAAAATCAGTTTGCCAGCGCCGCCTTCTGCGTCGCTACAATGGATTCGATTC‑CCCCTCGGGCCAGAGCCAACAAGATGAGt                                                                                                          >  2:800353/1‑129 (MQ=255)

                                   cATCTTACTTTTCTACAGACAAAAAAAAGGCGACTCATCAGTCGCCTTAAAAATCAGTTTGCCAGCGCCGCCTTCTGCGTCGCTACAATGGATTCGATTC‑CCCCTCGGGCCAGAGCCAACAAGATGAGt                                                                                                          <  1:800353/129‑1 (MQ=255)

                                             ttCTACAGACAAAAAAAAGGCGACTCATCAGTCGCCTTAAAAATCAGTTTGCCAGCGCCGCCTTCTGCGTCGCTACAATGGATTCGATTC‑CCCCTCGGGCCAGAGCCAACAAGATGAGTAGCTCTTCATGGGTGAACGGc                                                                                     <  1:884355/140‑1 (MQ=255)

                                                tACAGACAAAAAAAAGGCGACTCATCAGTCGCCTTAAAAATCAGTTTGCCAGCGCCGCCTTCTGCGTCGCTACAATGGATTCGATTC‑CCCCTCGGGCCAGAGCCAACAAGATGAGTAGCTCTTCATGGGTGAACGGCTCg                                                                                  >  1:670958/1‑140 (MQ=255)

                                                  cAGACAAAAAAAAGGCGACTCAGCACTCGGCTTAAAAGTCAGTTTGCCAGCGCCGCCTTCTGCGTCGCTACAATGGATTCGATTC‑CCCCTCGGGCCAGAGCCAACAAGATGAGTAGCTCTTCATGGGTGAACGGCTCGcc                                                                                <  1:405503/140‑1 (MQ=255)

                                                       aaaaaaaaGGCGACTCATCAGTCGCCTTAAAAATCAGTTTGCCAGCGCCGCCTTCTGCGTCGCTACAATGGATTCGATTC‑CCCCTCGGGCCGGAGCCAACAAGAGGAGAAGCTCTTCGTGGGTGAACGGCTCGCCTTCTg                                                                           >  2:405503/1‑140 (MQ=255)

                                                       aaaaaaaaGGCGACTCATCAGTCGCCTTAAAAATCAGTTTGCCAGCGCCGCCTTCTGCGTCGCTACAATGGATTCGATTC‑CCCCTCGGGCCAGAGCCAACAAGATGAGTAGCTCTTCATGGGTGAACGGCTCGCCTTCTg                                                                           >  1:5260/1‑140 (MQ=255)

                                                         aaaaaaGGCGACTCATCAGTCGCCTTAAAAATCAGTTTGCCAGCGCCGCCTTCTGCGTCGCTACAATGGATTCGATTC‑CCCCTCGGGCCAGAGCCAACAAGATGAGTAGCTCTTCATGGGTGAACGGCTCGCCTTCTGcc                                                                         <  2:844744/140‑1 (MQ=255)

                                                         aaaaaaGGCGACTCATCAGTCGCCTTAAAAATCAGTTTGCCAGCGCCGCCTTCTGCGTCGCTACAATGGATTCGATTC‑CCCCTCGGGCCAGAGCCAACAAGATGAGTAGCTCTTCATGGGTGAACGGCTCGCCTTCTGcc                                                                         <  2:934219/140‑1 (MQ=255)

                                                          aaaaaGGCGACTCATCAGTCGCCTTAAAAATCAGTTTGCCAGCGCCGCCTTCTGCGTCGCTACAATGGATTCGATTC‑CCCCTCGGGCCAGAGCCAACAAGATGAGTAGCTCTTCATGGGTGAACGGCTCGCCTTCTGCCg                                                                        <  2:903787/140‑1 (MQ=255)

                                                                 cGACTCATCAGTCGCCTTAAAAATCAGTTTGCCAGCGCCGCCTTCTGCGTCGCTACAATGGATTCGATTC‑CCCCTCGGGCCAGAGCCAACAAGATGAGTAGCTCTTCATGGGTGAACGGCTCGCCTTCTGCCGTCCCCTg                                                                 <  2:112443/140‑1 (MQ=255)

                                                                              gCCTTAAAAATCAGTTTGCCAGCGCCGCCTTCTGCGTCGCTACAATGGATTCGATTC‑CCCCTCGGGCCAGAGCCAACAAGATGAGTAGCTCTTCATGGGTGAACGGCTCGCCTTCTGCCGTCCCCTGCACTTCAatgatg                                                    >  2:57201/1‑140 (MQ=255)

                                                                              gCCTTAAAAATCAGTTTGCCAGCGCCGCCTTCTGCGTCGCTACAATGGATTCGATTC‑CCCCTCGGGCCAGAGCCAACAAGATGAGTAGCTCTTCATGGGTGAACGGCTCGCCTTCTGCCGTCCCCTGCACTTCAatgatg                                                    >  1:188053/1‑140 (MQ=255)

                                                                                 ttAAAAATCAGTTTGCCAGCGCCGCCTTCTGCGTCGCTACAATGGATTCGATTC‑CCCCTCGGGCCAGAGCTAACAAGATGAGTAGCTCTTCATGGGTGAACGGCTCGCCTTCTGCCGTCCCCTGCACTTCAATGATgcgc                                                 >  1:669627/1‑140 (MQ=255)

                                                                                   aaaaaTCAGTTTGCCAGCGCCGCCTTCTGCGTCGCTACAATGGATTCGATTC‑CCCCTCGGGCCAGAGCCAACAAGATGAGTAGCTCTTCATGGGTGAACGGCTCGCCTTCTGCCGTCCCCTGCACTTCAATGATGCGccc                                               >  1:2123/1‑140 (MQ=255)

                                                                                    aaaaTCAGTTTGCCAGCGCCGCCTTCTGCGTCGCTACAATGGATTCGATTC‑CCCCTCGGGCCAGAGCCAACAAGATGAGTAGCTCTTCATGGGTGAACGGCTCGCCTTCTGCCGTCCCCTGCACTTCAATGATGCGCCCg                                              <  2:545443/140‑1 (MQ=255)

                                                                                       aTCAGTTTGCCAGCGCCGCCTTCTGCGTCGCTACAATGGATTCGATTC‑CCCCTCGGGCCAGAGCCAACAAGATGAGTAGCTCTTCATGGGTGAACGGCTCGCCTTCTGCCGTCCCCTGCACTTCAATGATGCGCCCGTCt                                           <  2:138310/140‑1 (MQ=255)

                                                                                          aGTTTGCCAGCGCCGCCTTCTGCGTCGCTACAATGGATTCGATTC‑CCCCTCGGGCCAGAGCCAACAAGATGAGTAGCTCTTCATGGGTGAACGGCTCGCCTTCTGCCGTCCCCTGCACTTCAATGATGCGCCCGTCTTCg                                        <  1:555869/140‑1 (MQ=255)

                                                                                           gTTTGCCAGCGCCGCCTTCTGCGTCGCTACAATGGATTCGATTC‑CCCCTCGGGCCAGAGCCAACAAGATGAGTAGCTCTTCATGGGTGAACGGCTCGCCTTCTGCCGTCCCCTGCACTTCAATGATGCGCCCGTCTTCgg                                       <  1:57201/140‑1 (MQ=255)

                                                                                                      ccgccTTCTGCGTCGCTACAATGGATTCGATTC‑CCCCTCGGGCCAGAGCCAACAAGATGAGTAGCTCTTCATGGGTGAACGGCTCGCCTTCTGCCGTCCCCTTCACTTCAGTGATGCGCCCGTCATCGGTCATCACTACg                            >  1:476733/1‑140 (MQ=255)

                                                                                                      ccgccTTCTGCGTCGCTACAATGGATTCGATTC‑CCCCTCGGGCCAGAGCCAACAAGATGAGTAGCTCTTCATGGGTGAACGGCTCGCCTTCTGCCGTCCCCTGCACTTCAATGATGCGCCCGTCTTCGGTCATCACTACg                            >  1:757373/1‑140 (MQ=255)

                                                                                                       cgccTTCTGCGTCGCTACAATGGATTCGATTC‑CCCCTCGTGCCAGAGCCAACAAGATGAGTAGCTCTTCATGGGTGAACGGCTCGCCTTCTGCCGTCCCCTGCACTTCAATGATGCGCCCGTCTTCGGTCATCACTACGt                           <  2:980280/140‑1 (MQ=255)

                                                                                                         ccTTCTGCGTCGCTACAATGGATTCGATTC‑CCCCTCGGGCCAGAGCCAGCAAGATGAGTAGCTCTTCATGGGTGAACGGCTCGCCTTCTGCCGTCCCCTGCACTTCAATGATGCGCCCGTCTTCGGTCATCACTACGTTc                         <  1:240554/140‑1 (MQ=255)

                                                                                                                cGTCGCTACAATGGATTCGATTCCCCCCTCGGGCCAGAGCCAACAAGATGAGTAGCTCTTCATGGGTGAACGGCTCGCCTTCTGCCGTCCCCTGCACTTCAATGATGCGCCCGTCTTCGGTCATCACTACGTTCATGTCg                   >  2:999503/1‑140 (MQ=255)

                                                                                                                 gTCGCTACAATGGATTTGATTC‑CCCCTCGGGCCGGAGCCAACAAGATGTGTAGCTCTTCATGGGTGAACGGCTCGCCTTCTGCCGTCCCCTGCACTTCAATGATGCGCCCGTCTTCGGTCATCACTACGTTCATGTCGGt                 <  2:472003/140‑1 (MQ=255)

                                                                                                                 gTCGCTACAATGGATTCGATTC‑CCCCTCGGGCCAGAGCCAACAAGATGAGTAGCTCTTCATGGGTGAACGGCTCGCCTTCTGCCGTCCCCTGCACTTCAATGATGCGCCCGTCTTCGGTCATCACTACGTTCATGTCGGt                 <  2:757373/140‑1 (MQ=255)

                                                                                                                    gCTACAATGGATTCGATTC‑CCCCTCGGGCCAGAGCCAACAAGATGAGTAGCTCTTCATGGGTGAACGGCTCGCCTTCTGCCGTCCCCTGCAGTTCAATGATGCGGCCGACTTCGGTCGTCACCACGTTCATGTCGGtctc              >  2:355160/1‑140 (MQ=255)

                                                                                                                     cTACAATGGATTCGATTC‑CCCCTCGGGCCAGAGCCAACAAGATGAGTAGCTCTTCATGGGTGAACGGCTCGCCTTCTGCCGTCCCCTGCACTTCAATGATGCGCCCGTCTTCGGTCATCACt                               >  2:492293/1‑122 (MQ=255)

                                                                                                                     cTACAATGGATTCGATTC‑CCCCTCGGGCCAGAGCCAACAAGATGAGTAGCTCTTCATGGGTGAACGGCTCGCCTTCTGCCGTCCCCTGCACTTCAATGATGCGCCCGTCTTCGGTCATCACt                               <  1:492293/122‑1 (MQ=255)

                                                                                                                            ggATTCGATTC‑CCCCTCGGGCCAGAGCCAACAAGATGAGTAGCTCTTCATGGGTGAACGGCTCGCCTTCTGCCGTCCCCTGCACTTCAATGATGCGCCCGTCTTCGGTCATCACTACGTTCATGTCGGTCTCTGCGGCag      <  2:2123/140‑1 (MQ=255)

                                                                                                                             gattcgattc‑CCCCTCGGGCCAGAGCCAACAAGATGAGTAGCTCTTCATGGGTGAACGGCTCGCCTTCTGCCGTCCCCTGCACTTCAATGAGGCGCCCGTATTCGGTCATCACTACGTTCATTTCGGTCTCTGCGGCaga     >  2:336687/1‑140 (MQ=255)

                                                                                                                                tcgattc‑CCCCTCGGGCCAGAGCCAACAAGATGAGTAGCTCTTCATGGGTGAACGGCTCGCCTTCTGCCGTCCCCTGCACTTCAATGATGCGCCCGTCTTCGGTCATCACTACGTTCATGTCGGTCTCTGCGGCAGAGTc  >  1:654148/1‑140 (MQ=255)

                                                                                                                                tcgattc‑CCCCTCGGGCCAGAGCCAACAAGATGAGTAGCTCTTCATGGGTGAACGGCTCGCCTTCTGCCGTCCCCTGCACTTCAATGATGCGCCCGTCTTCGGTCATCACTACGTTCATGTCGGTCTCTGCGGCAGAGTc  >  1:975558/1‑140 (MQ=255)

                                                                                                                                tcgattc‑CCCCTCGGGCCAGAGCCAACAAGATGAGTAGCTCTTCATGGGTGAACGGCTCGCCTTCTGCCGTCCCCTGCACTTCAATGATGCGCCCGTCTTCGGTCATCACTACGTTCATGTCGGTCTCTGCGGCAGAGTc  >  1:238380/1‑140 (MQ=255)

AACTGGCGCTGATATGGTTTCATGCCTTCGCTCCTCATCTTACTTTTCTACAGACAAAAAAAAGGCGACTCATCAGTCGCCTTAAAAATCAGTTTGCCAGCGCCGCCTTCTGCGTCGCTACAATGGATTCGATT‑‑CCCCTCGGGCCAGAGCCAACAAGATGAGTAGCTCTTCATGGGTGAACGGCTCGCCTTCTGCCGTCCCCTGCACTTCAATGATGCGCCCGTCTTCGGTCATCACTACGTTCATGTCGGTCTCTGCGGCAGAGTC  >  NC_000913/3815746‑3816012

Alignment Legend
Aligned base mismatch/match (shaded by quality score): `ATCG/ATCG` `< 3 ≤` `ATCG/ATCG` `< 15 ≤` `ATCG/ATCG` `< 33 ≤` `ATCG/ATCG` `< 37 ≤` `ATCG/ATCG` `< 40 ≤` `ATCG/ATCG`
Unaligned base: `atcg` Masked matching base: `atcg` Alignment gap: `‑` Deleted base: `‑`

GATK/CNVnator alignment

N/A