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 F171 I0 R2	49	45.2	1012374	92.5%	936445	139.6

Breseq alignment

BRESEQ :: Evidence

Predicted mutation
evidence	seq id	position	mutation	freq	annotation	gene	description
RA	CP000730	39,653	C→A	100%	S494I (AGT→ATT)	mecA ←	penicillin binding protein 2 prime

Read alignment evidence...
	seq id	position		ref	new	freq	score (cons/poly)	reads	annotation	genes	product
*	CP000730	39,653	0	C	A	100.0%	184.6 / NA	53	S494I (AGT→ATT)	mecA	penicillin binding protein 2 prime
Reads supporting (aligned to +/- strand): ref base C (0/0); new base A (23/30); total (23/30)
Rejected as polymorphism: Frequency below/above cutoff threshold.
Rejected as polymorphism: Variant not supported by required number of reads on each strand.

CTAATGCGCTATAGATTGAAAGGATCTGTACTGGGTTAATCAGTATTTCACCTTGTCCGTAACCTGAATCAGCTAATAATATTTCATTATCTAAATTTTTGTTTGAAATTTGAGCATTATAAAATGGATAATCACTTGGTATATCTTCACCAACACCTAGTTTTTTCATGCCTTTTTCAAATTTCTTACTGCCTAATTCGAGTGCTACTCTAGCAAAGAAAATGTTATCTGATGATTCTATTGCTTGTTTTAAGTCGATATTACCATTTA  >  CP000730/39519‑39788

cTAATGCGCTATAGATTGAAAGGATCTGTACTGGGTTAATCAGTATTTCACCTTGTCCGTAACCTGAATCAGCTAATAATATTTCATTATCTAAATTTTTGTTTGAAATTTGAGCATTATAAAATGGATAATCAATTGGta                                                                                                                                   <  1:476559/141‑1 (MQ=255)

cTAATGCGCTATAGATTGAAAGGATCTGTACTGGGTTAATCAGTATTTCACCTTGTCCGTAACCTGAATCAGCTAATAATATTTCATTATCTAAATTTTTGTTTGAAATTTGAGCATTATAAAATGGATAATCAATTGGta                                                                                                                                   <  1:422367/141‑1 (MQ=255)

cTAATGCGCTATAGATTGAAAGGATCTGTACTGGGTTAATCAGTATTTCACCTTGTCCGTAACCTGAATCAGCTAATAATATTTCATTATCTAAATTTTTGTTTGAAATTTGAGCATTATAAAATGGATAATCAATTGGta                                                                                                                                   >  1:89550/1‑141 (MQ=255)

    tGCGCTATAGATTGAAAGGATCTGTACTGGGTTAATCAGTATTTCACCTTGTCCGTAACCTGAATCAGCTAATAATATTTCATTATCTAAATTTTTGTTTGAAATTTGAGCATTATAAAATGGATAATCAATTGGTATATc                                                                                                                               <  1:89961/141‑1 (MQ=255)

            aGATTGAAAGGATCTGTACTGGGTTAATCAGTATTTCACCTTGTCCGTAACCTGAATCAGCTAATAATATTTCATTATCTAAATTTTTGTTTGAAATTTGAGCATTATAAAATGGATAATCAATTGGTATATCTTCACCaa                                                                                                                       <  2:419781/141‑1 (MQ=255)

                  aaaGGATCTGTACTGGGTTAATCAGTATTTCACCTTGTCCGTAACCTGAATCAGCTAATAATATTTCATTATCTAAATTTTTGTTTGAAATTTGAGCATTATAAAATGGATAATCAATTGGTATATCTTCACCAACACCTa                                                                                                                 >  2:496967/1‑141 (MQ=255)

                               tGGGTTAATCAGTATTTCACCTTGTCCGTAACCTGAATCAGCTAATAATATTTCATTATCTAAATTTTTGTTTGAAATTTGAGCATTATAAAATGGATAATCAATTGGTATATCTTCACCAACACCTAGTTTTTTCATGcc                                                                                                    <  1:101658/141‑1 (MQ=255)

                                gggTTAATCAGTATTTCACCTTGTCCGTAACCTGAATCAGCTAATAATATTTCATTATCTAAATTTTTGTTTGAAATTTGAGCATTATAAAATGGATAATCAATTGGTATATCTTCACCAACACCTAGTTTTTTCATGCCt                                                                                                   >  2:487654/1‑141 (MQ=255)

                                          gTATTTCACCTTGTCCGTAACCTGAATCAGCTAATAATATTTCATTATCTAAATTTTTGTTTGAAATTTGAGCATTATAAAATGGATAATCAATTGGTATATCTTCACCAACACCTAGTTTTTTCATGCCTTTTTCAAAtt                                                                                         >  2:7007/1‑141 (MQ=255)

                                                cACCTTGTCCGTAACCTGAATCAGCTAATAATATTTCATTATCTAAATTTTTGTTTGAAATTTGAGCATTATAAAATGGATAATCAATTGGTATATCTTCACCAACACCTAGTTTTTTCATGCCTTTTTCAAATTTCTTAc                                                                                   >  2:53/1‑141 (MQ=255)

                                                 aCCTTGTCCGTAACCTGAATCAGCTAATAATATTTCATTATCTAAATTTTTGTTTTTTTTTTGAGCATTATAAAATGGATAATCAATTGGTATATCTTCACCAACACCTAGTTTTTTCATGCCTTTTTCAAATTTCTTACt                                                                                  >  2:105344/1‑141 (MQ=255)

                                                 aCCTTGTCCGTAACCTGAATCAGCTAATAATATTTCATTATCTAAATTTTTGTTTGAAATTTGAGCATTATAAAATGGATAATCAATTGGTATATCTTCACCAACACCTAGTTTTTTCATGCCTTTTTCAAATTTCTTACt                                                                                  >  2:251785/1‑141 (MQ=255)

                                                   cTTGTCCGTAACCTGAATCAGCTAATAATATTTCATTATCTAAATTTTTGTTTGAAATTTGAGCATTATAAAATGGATAATCAATTGGTATATCTTCACCAACACCTAGTTTTTTCATGCCTTTTTCAAATTTCTTACTGc                                                                                <  1:395623/141‑1 (MQ=255)

                                                      gTCCGTAACCTGAATCAGCTAATAATATTTCATTATCTAAATTTTTTTTTTTTTTTTTAGCATTATAAAATGGATAATCAATTGGTATATCTTCACCAACACCTAGTTTTTTCATGCCTTTTTCTTATTTCTTACTGCCTa                                                                             >  2:88601/1‑141 (MQ=255)

                                                      gTCCGTAACCTGAATCAGCTAATAATATTTCATTATCTAAATTTTTGTTTGAAATTTGAGCATTATAAAATGGATAATCAATTGGTATATCTTCACCAACACCTAGTTTTTTCATGCCTTTTTCAAATTTCTTACTGCCTa                                                                             >  1:433623/1‑141 (MQ=255)

                                                        ccGTAACCTGAATCAGCTAATAATATTTCATTATCTAAATTTTTTTTTTTTTTTTGATCATTATAAAATGGATAATCAATTTGTATATCTTCTCCAACACCTAGTTTTTTCATGCCTTTTTTAAATTTCTTACTGCCTAAt                                                                           >  2:153777/1‑141 (MQ=255)

                                                         cGTAACCTGAATCAGCTAATAATATTTCATTATCTAAATTTTTGTTTGAAATTTGAGCATTATAAAATGGATAATCAATTGGTATATCTTCACCAACACCTAGTTTTTTCATGCCTTTTTCAAATTTCTTATTGCCTAAtt                                                                          >  1:259009/1‑141 (MQ=255)

                                                           tAACCTGAATCAGCTAATAATATTTCATTATCTAAATTTTTGTTTGAAATTTGAGCATTATAAAATGGATAATCAATTGGTATATCTTCACCAACACCTAGTTTTTTCATGCCTTTTTCAAATTTCTTACTGCCTAATTCg                                                                        <  2:88199/141‑1 (MQ=255)

                                                             aCCTGAATCAGCTAATAATATTTCATTATCTAAATTTTTGTTTGAAATTTGAGCATTATAAAATGGATAATCAATTGGTATATCTTCACCAACACCTAGTTTTTTCATGCCTTTTTCAATTTTCTTACTGCCTAATTCGat                                                                      >  2:104274/1‑140 (MQ=255)

                                                              ccTGAATCAGCTAATAATATTTCATTATCTAAATTTTTGTTTGAAATTTGAGCATTATAAAATGGATAATCAATTGGTATATCTTCACCAACACCTAGTTTTTTCATGCCTTTTTCAAATTTCTTACTGCCTAATTCGAGt                                                                     <  2:241330/141‑1 (MQ=255)

                                                              ccTGAATCAGCTAATAATATTTCATTATCTAAATTTTTGTTTGAAATTTGAGCATTATAAAATGGATAATCAATTGGTATATCTTCACCAACACCTAGTTTTTTCATGCCTTTTTCAAATTTCTTACTGCCTAATTCGAGt                                                                     <  2:329042/141‑1 (MQ=255)

                                                               cTGAATCAGCTAATAATATTTCATTATCTAAATTTTTGTTTGAAATTTGAGCATTATAAAATGGATAATCAATTGGTATATCTTCACCAACACCTAGTTTTTTCATGCCTTTTTCAAATTTCTTACTGCCTAATTCGAGTg                                                                    <  1:12092/141‑1 (MQ=255)

                                                                tGAATCAGCTAATAATATTTCATTATCTAAATTTTTGTTTGAAATTTGAGCATTATAAAATGGATAATCAATTGGTATATCTTCACCAACACCTAGTTTTTTCATGCCTTTTTCAAATTTCTTACTGCCTAATTCGAGTGc                                                                   <  2:277679/141‑1 (MQ=255)

                                                                  aaTCAGCTAATAATATTTCATTATCTAAATTTTTGTTTGAAATTTGAGCATTATAAAATGGATAATCAATTGGTATATCTTCACCAACACCTAGTTTTTTCATGCCTTTTTCAAATTTCTTACTGCCTAATTCGAGTGCTa                                                                 >  1:454853/1‑141 (MQ=255)

                                                                   aTCAGCTAATAATTTTTCATTATCTAAATTTTTGTTTGAAATTTGAGCATTATAAAATGGATAATCAATTGGTATATCTTCACCAACACCTAGTTTTTTCATGCCTTTTTCAAATTTCTTACTGCCTAATTCGAGTGCTAc                                                                <  2:59284/141‑1 (MQ=255)

                                                                   aTCAGCTAATAATATTTCATTATCTAAATTTTTGTTTGAAATTTGAGCATTATAAAATGGATAATCAATTGGTATATCTTCACCAACACCTAGTTTTTTCATGCCTTTTTCAAATTTCTTACTGCCTAATTCGAGTGCTAc                                                                <  2:110911/141‑1 (MQ=255)

                                                                                atTTCATTATCTAAATTTTTGTTTGAAATTTGAGCATTATAAAATGGATAATCAATTGGTATATCTTCACCAACACCTAGTTTTTTCATGCCTTTTTCAAATTTCTTACTGCCTAATTCGAGTGCTACTCTAGCAAAGaaa                                                   >  1:242690/1‑141 (MQ=255)

                                                                                 tttCATTATCTAAATTTTTGTTTGAAATTTGAGCATTATAAAATGGATAATCAATTGGTATATCTTCACCAACACCTAGTTTTTTCATGCCTTTTTCAAATTTCTTACTGCCTAATTCGAGTGCTACTCTAGCAAAGaaaa                                                  >  1:189148/1‑141 (MQ=255)

                                                                                    cATTATCTAAATTTTTGTTTGAAATTTGAGCATTATAAAATGGATAATCAATTGGTATATCTTCACCAACACCTAGTTTTTTCATGCCTTTTTCAAATTTCTTACTGCCTAATTCGAGTGCTACTCTAGCAAAGAAAATGt                                               <  2:303566/141‑1 (MQ=255)

                                                                                     aTTATCTAAATTTTTGTTTGAAATTTGAGCATTATAAAATGGATAATCAATTGGTATATCTTCACCAACACCTAGTTTTTTCATGCCTTTTTCAAATTTCTTACTGCCTAATTCGAGTGCTACTCTATCAAAGAAAATGtt                                              >  2:302356/1‑141 (MQ=255)

                                                                                           tAAATTTTTGTTTGAAATTTGAGCATTATAAAATGGATAATCAATTGGTATATCTTCACCAACACCTAGTTTTTTCATGCCTTTTTCAAATTTCTTACTGCCTAATTCGAGTGCTACTCTAGCAAAGAAAATGTTATCtga                                        <  2:154615/141‑1 (MQ=255)

                                                                                           tAAATTTTTGTTTGAAATTTGAGCATTATAAAATGGATAATCAATTGGTATATCTTCACCAACACCTAGTTTTTTCATGCCTTTTTCAAATTTCTTACTGCCTAATTCGAGTGCTACTCTAGCAAAGAAAATGTTATCtga                                        >  1:47576/1‑141 (MQ=255)

                                                                                              aTTTTTGTTTGAAATTTGAGCATTATAAAATGGATAATCAATTGGTATATCTTCACCAACACCTAGTTTTTTCATGCCTTTTTCAAATTTCTTACTGCCTAATTCGAGTGCTACTCTAGCAAAGAAAATGTTATCtgatga                                     <  1:321309/141‑1 (MQ=255)

                                                                                               tttttGTTTGAAATTTGAGCATTATAAAATGGATAATCAATTGGTATATCTTCACCAACACCTAGTTTTTTCATGCCTTTTTCAAATTTCTTACTGCCTAATTCGAGTGCTACTCTAGCAAAGAAAATGTTATCTgatgat                                    <  1:31767/141‑1 (MQ=255)

                                                                                                ttttGTTTGAAATTTGAGCATTATAAAATGGATAATCAATTGGTATATCTTCACCAACACCTAGTTTTTTCATGCCTTTTTCAAATTTCTTACTGCCTAATTCGAGTGCTACTCTAGCAAAGAAAATGTTATCTGATGAtt                                   <  2:261505/141‑1 (MQ=255)

                                                                                                ttttGTTTGAAATTTGAGCATTATAAAATGGATAATCAATTGGTATATCTTCACCAACACCTAGTTTTTTCATGCCTTTTTCAAATTTCTTACTGCCTAATTCGAGTGCTACTCTAGCAAAGAAAATGTTATCTGATGAtt                                   <  1:258125/141‑1 (MQ=255)

                                                                                                ttttGTTTGAAATTTGAGCATTATAAAATGGATAATCAATTGGTATATCTTCACCAACACCTAGTTTTTTCATGCCTTTTTCAAATTTCTTACTGCCTAATTCGAGTGCTACTCTAGCAAAGAAAATGTTATCTGATGAtt                                   <  2:9770/141‑1 (MQ=255)

                                                                                                ttttGTTTGAAATTTGAGCATTATAAAATGGATAATCAATTGGTATATCTTCACCAACACCTAGTTTTTTCATGCCTTTTTCAAATTTCTTACTGCCTAATTCGAGTGCTACTCTAGCAAAGAAAATGTTATCTGATGAtt                                   <  2:168402/141‑1 (MQ=255)

                                                                                                  ttgtttgAAATTTGAGCATTATAAAATGGATAATCAATTGGTATATCTTCACCAACACCTAGTTTTTTCATGCCTTTTTCAAATTTCTTACTGCCTAATTCGAGTGCTACTCTAGCAAAGAAAATGTTATCTGATGATTCt                                 <  1:324371/141‑1 (MQ=255)

                                                                                                    gtttgAAATTTGAGCATTATAAAATGGATAATCAATTGGTATATCTTCACCAACACCTAGTTTTTTCATGCCTTTTTCAAATTTCTTACTGCCTAATTCGAGTGCTACTCTAGCAAAGAAAATGTTATCTGATGATTCTAt                               >  1:253642/1‑141 (MQ=255)

                                                                                                     tttgAAATTTGAGCATTATAAAATGGATAATCAATTGGTATATCTTCACCAACACCTAGTTTTTTCATGCCTTTTTCAAATTTCTTACTGCCTAATTCGAGTGCTACTCTAGCAAAGAAAATGTTATCTGATGATTCTAtt                              >  2:302768/1‑141 (MQ=255)

                                                                                                      ttgAAATTTGAGCATTATAAAATGGATAATCAATTGGTATATCTTCACCAACACCTAGTTTTTTCATGCCTTTTTCAAATTTCTTACTGCCTAATTCGAGTGCTACTCTAGCAAAGAAAATGTTATCTGATGATTCTATTg                             >  1:494665/1‑141 (MQ=255)

                                                                                                       tgAAATTTGAGCATTATAAAATGGATAATCAATTGGTATATCTTCACCAACACCTAGTTTTTTCATGCCTTTTTCAAATTTCTTACTGCCTAATTCGAGTGCTACTCTAGCAAAGAAAATGTTATCTGATGATTCTATTGc                            <  1:290070/141‑1 (MQ=255)

                                                                                                       tgAAATTTGAGCATTATAAAATGGATAATCAATTGGTATATCTTCACCAACACCTAGTTTTTTCATGCCTTTTTCAAATTTCTTACTGCCTAATTCGAGTGCTACTCTAGCAAAGAAAATGTTATCTGATGATTCTATTGc                            <  2:245659/141‑1 (MQ=255)

                                                                                                         aaaTTTGAGCATTATAAAATGGATAATCAATTGGTATATCTTCACCAACACCTAGTTTTTTCATGCCTTTTTCAAATTTCTTACTGCCTAATTCGAGTGCTACTCTAGCAAAGAAAATGTTATCTGATGATTCTATTGCtt                          <  2:47576/141‑1 (MQ=255)

                                                                                                            tttGAGCATTATAAAATGGATAATCAATTGGTATATCTTCACCAACACCTAGTTTTTTCATGCCTTTTTCAAATTTCTTACTGCCTAATTCGAGTGCTACTCTAGCAAAGAAAATGTTATCTGATGATTCTATTGCTTGtt                       <  1:450560/141‑1 (MQ=255)

                                                                                                             ttGAGCATTATAAAATGGATAATCAATTGGTATATCTTCACCAACACCTAGTTTTTTCATGCCTTTTTCAAATTTCTTACTGCCTAATTCGAGTGCTACTCTAGCAAAGAAAATGTTATCTGATGATTCTATTGCTTGttt                      <  2:253642/141‑1 (MQ=255)

                                                                                                               gAGCATTATAAAATGGATAATCAATTGGTATATCTTCACCAACACCTAGTTTTTTCATGCCTTTTTCAAATTTCTTACTGCCTAATTCGAGTGCTACTCTAGCAAAGAAAATGTTATCTGATGATTCTATTGCTTGTTTTa                    >  1:352717/1‑141 (MQ=255)

                                                                                                               gAGCATTATAAAATGGATAATCAATTGGTATATCTTCACCAACACCTAGTTTTTTCATGCCTTTTTCAAATTTCTTACTGCCTAATTCGAGTGCTACTCTAGCAAAGAAAATGTTATCTGATGATTCTATTGCTTGTTTTa                    <  1:372836/141‑1 (MQ=255)

                                                                                                                               aTAATCAATTGGTATATCTTCACCAACACCTAGTTTTTTCATGCCTTTTTCAAATTTCTTACTGCCTAATTCGAGTGCTACTCTAGCAAAGAAAATGTTATCTGATGATTCTATTGCTTGTTTTAAGTCGATATTACCAtt    <  2:394566/141‑1 (MQ=255)

                                                                                                                               aTAATCAATTGGTATATCTTCACCAACACCTAGTTTTTTCATGCCTTTTTCAAATTTCTTACTGCCTAATTCGAGTGCTACTCTAGCAAAGAAAATGTTATCTGATGATTCTATTGCTTGTTTTAAGTCGATATTACCAtt    <  2:454853/141‑1 (MQ=255)

                                                                                                                                 aaTCAATTGGTATATCTTCACCAACACCTAGTTTTTTCATGCCTTTTTCAAATTTCTTACTGCCTAATTCGAGTGCTACTCTAGCAAAGAAAATGTTATCTGATGATTCTATTGCTTGTTTTAAGTCGATATTACCATTTa  >  2:92059/1‑141 (MQ=255)

                                                                                                                                 aaTCAATTGGTATATCTTCACCAACACCTAGTTTTTTCATGCCTTTTTCAAATTTCTTACTGCCTAATTCGAGTGCTACTCTAGCAAAGAAAATGTTATCTGATGATTCTATTGCTTGTTTTAAGTCGATATTACCATTTa  >  1:86616/1‑141 (MQ=255)

CTAATGCGCTATAGATTGAAAGGATCTGTACTGGGTTAATCAGTATTTCACCTTGTCCGTAACCTGAATCAGCTAATAATATTTCATTATCTAAATTTTTGTTTGAAATTTGAGCATTATAAAATGGATAATCACTTGGTATATCTTCACCAACACCTAGTTTTTTCATGCCTTTTTCAAATTTCTTACTGCCTAATTCGAGTGCTACTCTAGCAAAGAAAATGTTATCTGATGATTCTATTGCTTGTTTTAAGTCGATATTACCATTTA  >  CP000730/39519‑39788

Alignment Legend
Aligned base mismatch/match (shaded by quality score): `ATCG/ATCG` `< 3 ≤` `ATCG/ATCG` `< 12 ≤` `ATCG/ATCG` `< 32 ≤` `ATCG/ATCG` `< 41 ≤` `ATCG/ATCG`
Unaligned base: `atcg` Masked matching base: `atcg` Alignment gap: `‑` Deleted base: `‑`

GATK/CNVnator alignment

N/A