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
A10 F1 I2 R1	757	38.1	1607544	96.5%	1551279	117.2

Breseq alignment

BRESEQ :: Evidence

Predicted mutation
evidence	seq id	position	mutation	annotation	gene	description
RA	NC_000913	2,484,897	(C)_6→7	coding (524/3594 nt)	evgS →	hybrid sensory histidine kinase in two‑component regulatory system with EvgA

Read alignment evidence...
	seq id	position		ref	new	freq	score (cons/poly)	reads	annotation	genes	product
*	NC_000913	2,484,891	1	.	C	95.5%	150.7 / 0.1	44	coding (518/3594 nt)	evgS	hybrid sensory histidine kinase in two‑component regulatory system with EvgA
Reads supporting (aligned to +/- strand): ref base . (1/1); new base C (20/22); total (21/23)
Fisher's exact test for biased strand distribution p-value = 1.00e+00
Kolmogorov-Smirnov test that lower quality scores support variant p-value = 9.25e-01

TTCGCCGCCTCTTAATAATGACATTGCTGCAACCAAACCATTGATAATTACCTTTCCGGCGCTGGTAACCACCCTTCACGACTCAATGCGACCGCTTACCTCACCAAAACCAGTAAATATTGCTCGGGTAGCAAATTA‑CCCC‑C‑CAGACGAGGTAATTCATCAATCATTTCCAAAAGCAACAATTATCTCTTTTACAAATTTATATCAGGCATTAGCATCCGTCTCAGCTGGGCACAATGATTACTTTATTGGTAGTAACATCATTAC  >  NC_000913/2484754‑2485020

ttCGCCGCCTCTTAATAATGACATTGCTGCAACCAAACCATTGATAATTACCTTTCCGGCGCTGGTAACCACCCTTCACGACTCAATGCGACCGCTTACCTCACCAAAACCAGTAAATATTGCTCGGGTAGCAAATTA‑c                                                                                                                                    >  2:215059/1‑139 (MQ=255)

  cgccgcCTCTTAATAATGACATTGCTGCAACCAAACCATTGATAATTACCTTTCCGGCGCTGGTAACCACCCTTCACGACTCAATGCGACCGCTTACCTCACCAAAACCAGTAAATATTGCTCGGGTAGCAAATTA‑ccc                                                                                                                                  >  1:716100/1‑139 (MQ=255)

           ttAATAATGACATTGCTGCAACCAAACCATTGATAATTACCTTTCCGGCGCTGGTAACCACCCTTCACGACTCAATGCGACCGCTTACCTCACCAAAACCAGTAAATATTGCTCGGGTAGCAAATTACCCCC‑C‑CAGACg                                                                                                                        <  2:278391/139‑1 (MQ=255)

              ataatGACATTGCTGCAACCAAACCATTGATAATTACCTTTCCGGTGCTGGTAACCACCCTTCACGACTCAATGCGACCGCTTACCTCACCAAAACCAGTAAATATTGCTCGGGTAGCAAATTACCCCC‑C‑CAGACGAgg                                                                                                                     <  1:492871/139‑1 (MQ=255)

               taatGACATTGCTGCAACCAAACCATTGATAATTACCTTTCCGGCGCTGGTAACCACCCTTCACGACTCAATGCGACCGCTTACCTCACCAAAACCAGTAAATATTGCTCGGGTAGCAAATTACCCCC‑C‑CAGACGAGGt                                                                                                                    <  2:189648/139‑1 (MQ=255)

                  tGACATTGCTGCAACCAAACCATTGATAATTACCTTTCCGGCGCTGGTAACCACCCTTCACGACTCAATGCGACCGCTTACCTCACCAAAACCAGTAAATATTGCTCGGGTAGCAAATTACCCCC‑C‑CAGACGAGGTAAt                                                                                                                 >  2:534518/1‑139 (MQ=255)

                     cATTGCTGCAACCAAACCATTGATAATTACCTTTCCGGCGCTGGTAACCACCCTTCACGACTCAATGCGACCGCTTACCTCA‑CAAAACCAGTAAATATTGCTCGGGTAGCAAATTACCCCC‑C‑CAGACGAGGTAATtcat                                                                                                             >  2:51069/1‑139 (MQ=255)

                      aTTGCTGCAACCAAACCATTGATAATTACCTTTCCGGCGCTGGTAACCACCCTTCACGACTCAATGCGACCGCTTACCTCACCAAAACCAGTAAATATTGCTCGGGTAGCAAATTACCCCC‑C‑CAGACGAGGTAATtcat                                                                                                             >  1:452079/1‑139 (MQ=255)

                         gctgcAACCAAACCATTGATAATTACCTTTCCGGCGCTGGTAACCACCCTTCACGACTCAATGCGACCGCTTACCTCACCAAAACCAGTAAATATTGCTCGGGTAGCAAATTACCCCC‑C‑CAGACGAGGTAATTCatcaa                                                                                                          >  1:147254/1‑139 (MQ=255)

                          ctgcAACCAAACCATTGATAATTACCTTTCCGGCGCTGGTAACCACCCTTCACGACTCAATGCGACCGCTTACCTCTCCAAAACCAGTAAATATTGCTCGGGTAGCAAATTACCCCC‑C‑CAGACGAGGTAATTCatcaat                                                                                                         >  1:574656/1‑139 (MQ=255)

                                ccaaaccaTTGATAATTACCTTTCCGGCGCTGGTAACCACCCTTCACGACTCAATGCGACCGCTTACCTCACCAAAACCAGTAAATATTGCTCGGGTAGCAAATTA‑CCCCAC‑CAGACGAGGTAATTCATCAATCATTTc                                                                                                   >  1:607017/1‑139 (MQ=255)

                                   aaccaTTGATAATTACCTTTCCGGCGCTGGTAACCACCCTTCACGACTCAATGCGACCGCTTACCTCACCAAAACCAGTAAATATTGCTCGGGTAGCAAATTACCCCC‑C‑CAGACGAGGTAATTCATCAATCATTTCCaa                                                                                                <  2:147254/139‑1 (MQ=255)

                                    accaTTGATAATTACCTTTCCGGCGCTGGTAACCACCCTTCACGACTCAATGCGACCGCTTACCTCACCAAAACCAGTAAATATTGCTCGGGTAGCAAATTACCCCC‑C‑CAGACGAGGTAATTCATCAATCATTTCCaaa                                                                                               >  1:767019/1‑139 (MQ=255)

                                        ttGATAATTACCTTTCCGGCGCTGGTAACCACCCTTCACGACTCAATGCGACCGCTTACCTCACCAAAACCAGTAAATATTGCTCGGGTAGCAAATTACCCCC‑C‑CAGACGAGGTAATTCATCAATCATTTCCAAAAGca                                                                                           >  2:108360/1‑139 (MQ=255)

                                                  ccTTTCCGGCGCTGGTAACCACCCTTCACGACTCAATGCGACCGCTTACCTCACCAAAACCAGTAAATATTGCTCGGGTAGCAAATTACCCCC‑C‑CAGACGAGGTAATTCATCAATCATTTCCAAAAGCAACAATTAtct                                                                                 <  2:83495/139‑1 (MQ=255)

                                                     ttCCGGCGCTGGTAACCACCCTTCACGACTCAATGCGACCGCTTACCTCACCAAAACCAGTAAATATTGCTCGGGTAGCAAATTACCCCC‑C‑CAGACg                                                                                                                        >  2:362658/1‑97 (MQ=255)

                                                     ttCCGGCGCTGGTAACCACCCTTCACGACTCAATGCGACCGCTTACCTCACCAAAACCAGTAAATATTGCTCGGGTAGCAAATTACCCCC‑C‑CAGACg                                                                                                                        <  1:362658/97‑1 (MQ=255)

                                                        cGGCGCTGGTAACCACCCTTCACGACTCAATGCGACCGCTTACCTCACCAAAACCAGTAAATATTGCTCGGGTAGCAAATTACCCCC‑C‑CAGACGAGGTAATTCATCAATCATTTCCAAAAGCAACAATTATCTCTTTTa                                                                           <  2:527010/139‑1 (MQ=255)

                                                        cGGCGCTGGTAACCACCCTTCACGACTCAATGCGACCGCTTACCTCACCAAAACCAGTAAATATTGCTCGGGTAGCAAATTACCCCC‑C‑CAGACGAGGTAATTCATCAATCATTTCCAAAAGCAACAATTATCTCTTTTa                                                                           <  1:534518/139‑1 (MQ=255)

                                                             cTGGTAACCACCCTTCACGACTCAATGCGACCGCTTACCTCACCAAAACCAGTAAATATTGCTCGGGTAGCAAATTACCCCC‑C‑CAGACGAGGTAATTCATCAATCATTTCCAAAAGCAACAATTATCTCTTTTACAAAt                                                                      >  1:532520/1‑139 (MQ=255)

                                                                    ccaccCTTCACGACTCAATGCGACCGCTTACCTCACCAAAACCAGTAAATATTGCTCGGGTAGCAAATTACCCCC‑C‑CAGACGAGGTAATTCATCAATCATTTCCAAAAGCAACAATTATCTCTTTTACAAATTTATATc                                                               <  2:334343/139‑1 (MQ=255)

                                                                       cccTTCACGACTCAATGCGACCGCTTACCTCACCAAAACCAGTAAATATTGCTCGGGTAGCAAATTACCCCC‑C‑CAGACGAGGTAATTCATCAATCATTTCCAAAAGCAACAATTATCTCTTTTACAAATTTATATCAgg                                                            >  1:38955/1‑139 (MQ=255)

                                                                       cccTTCACGACTCAATGCGACCGCTTACCTCACCAAAACCAGTAAATATTGCTCGGGTAGCAAATTACCCCC‑C‑CAGACGAGGTAATTCATCAATCACTTCCAAAAGCAACAATTATCTCTTTTACAAATTTATATCAgg                                                            <  1:215059/139‑1 (MQ=255)

                                                                        ccTTCACGACTCAATGCGACCGCTTACCTCACCAAAACCAGTAAATATTGCTCGGGTAGCAAATTACCCCC‑C‑CAGACGAGGTAATTCATCAATCATTTCCAAAAGCAACAATTATCTCTTTTACAAATTTATATCAGGc                                                           >  2:398551/1‑139 (MQ=255)

                                                                          ttCACGACTCAATGCGACCGCTTACCTCACCAAAACCAGTAAATATTGCTCGGGTAGCAAATTACCCCC‑C‑CAGACGAGGTAATTCATCAATCATTTCCAAAAGCAACAATTATCTCTTTTACAAATTTATATCAGGCAt                                                         >  1:726268/1‑139 (MQ=255)

                                                                          ttCACGACTCAATGCGACCGCTTACCTCACCAAAACCAGTAAATATTGCTCGGGTAGCAAATTACCCCC‑C‑CAGACGAGGTAATTCATCAATCATTTCCAAAAGCAACAATTATCTCTTTTACAAATTTATATCAGGCAt                                                         <  2:716100/139‑1 (MQ=255)

                                                                          ttCACGACTCAATGCGACCGCTTACCTCACCAAAACCAGTAAATATTGCTCGGGTAGCAAATTACCCCC‑C‑CAGACGAGGTAATTCATCAATCATTTCCAAAAGCAACAATTATCTCTTTTACAAATTTATATCAGGCAt                                                         >  2:137485/1‑139 (MQ=255)

                                                                                      tGCGACCGCTTACCTCACCAAAACCAGTAAATATTGCTCGGGTAGCAAATTACCCCC‑C‑CAGACGAGGTAATTCATCAATCATTTCCAAAAGCAACAATTATCTCTTTTACAAATTTATATCAGGCATTAGCATCCGtct                                             <  2:726268/139‑1 (MQ=255)

                                                                                      tGCGACCGCTTACCTCACCAAAACCAGTAAATATTGCTCGGGTAGCAAATTACCCCC‑C‑CAGACGAGGTAATTCATCAATCATTTCCAAAAGCAACAATTATCTCTTTTACAAATTTATATCAGGCATTAGCATCCGtct                                             >  2:574989/1‑139 (MQ=255)

                                                                                         gACCGCTTACCTCACCAAAACCAGTAAATATTGCTCGGGTAGCAAATTACCCCC‑C‑CAGACGAGGTAATTCATCAATCATTTCCAAAAGCAACAATTATCTCTTTTACAAATTTATATCAGGCATTAGCATCCGTCTCAg                                          <  1:601850/139‑1 (MQ=255)

                                                                                           ccGCTTACCTCACCAAAACCAGTAAATATTGCTCGGGTAGCAAATTACCCCC‑C‑CAGACGAGGTAATTCATCAATCATTTCCAAAAGcaa                                                                                          >  2:569729/1‑89 (MQ=255)

                                                                                           ccGCTTACCTCACCAAAACCAGTAAATATTGCTCGGGTAGCAAATTACCCCC‑C‑CAGACGAGGTAATTCATCAATCATTTCCAAAAGcaa                                                                                          <  1:569729/89‑1 (MQ=255)

                                                                                           ccGCTTACCTCACCAAAACCAGTAAATATTGCTCGGGTAGCAAATTACCCCC‑C‑CAGACGAGGTAATTCATCAATCATTTCCAAAAGCAACAATTATCTCTTTTACAAATTTATATCAGGCATTAGCATCCGTCTCAGCt                                        >  2:289286/1‑139 (MQ=255)

                                                                                           ccGCTTACCTCACCAAAACCAGTAAATATTGCTCGGGTAGCAAATTA‑CCCC‑CGCAGACGAGGTAATTCATCAATCATTTCCAAAAGCAACAATTATCTCTTTTACAAATTTATATCAGGCATTAGCATCCGTCTCAGCt                                        <  2:532520/139‑1 (MQ=255)

                                                                                              cTTACCTCACCAAAACCAGTAAATATTGCTCGGGTAGCAAATTACCCCC‑C‑CAGACGAGGTAATTCATCAATCATTTCCAAAAGCAACAATTATCTCTTTTACAAATTTATATCAGGCATTAGCATCCGTCTCAGCTggg                                     >  2:533260/1‑139 (MQ=255)

                                                                                               ttACCTCACCAAAACCAGTAAATATTGCTCGGGTAGCAAATTACCCCC‑C‑CAGACGAGGTAATTCATCAATCATTTCCAAAAGCAACAATTAACTCTTTTACAAATTTATATCAGGCATTAGCATCCGTCTCAGCTGGGc                                    <  1:574989/139‑1 (MQ=255)

                                                                                                 aCCTCACCAAAACCAGTAAATATTGCTCGGGTAGCAAATTACCCCC‑C‑CAAACGAGGTAATTCATCAATCATTTCCAAAAGCAACTATTATCTCTTTTACAAATTTATATCAGGCATTAGCATCCGTCTCAGCTGGGcac                                  <  2:607017/139‑1 (MQ=255)

                                                                                                      aCCAAAACCAGTAAATATTGCTCGGGTAGCAAATTACCCCC‑C‑CAGACGAGGTAATTCATCAATCATTTCCAAAAGCAACAATTATCTCTTTTACAAATTTATATCAGGCATTAGCATCCGTCTCAGCTGGGCACAATGa                             <  1:108360/139‑1 (MQ=255)

                                                                                                               aGTAAATATTGCTCGGGTAGCAAATTACCCCC‑C‑CAGACGAGGTAATTCATCAATCATTTCCAAAAGCAACAATTATCTCTTTTACAAATTTATATCAGGCATTAGCATCCGTCTCAGCTGGGCACAATGATTACTTTAt                    <  1:137485/139‑1 (MQ=255)

                                                                                                                gTAAATATTGCTCGGGTAGCAAATTACCCCC‑C‑CAGACGAGGTAATTCATCAATCATTTCCAAAAGCAACAATTATCTCTTTTACAAATTTATATCAGGCATTAGCATCCGtct                                             >  1:187005/1‑113 (MQ=255)

                                                                                                                gTAAATATTGCTCGGGTAGCAAATTACCCCC‑C‑CAGACGAGGTAATTCATCAATCATTTCCAAAAGCAACAATTATCTCTTTTACAAATTTATATCAGGCATTAGCATCCGtct                                             <  2:187005/113‑1 (MQ=255)

                                                                                                                        tGCTCGGGTAGCAAATTACCCCC‑C‑CAGACGAGGTAATTCATCAATCATTTCCAAAAGCAACAATTATCTCTTTTACAAATTTATATCAGGCATTAGCa                                                    >  2:583668/1‑98 (MQ=255)

                                                                                                                        tGCTCGGGTAGCAAATTACCCCC‑C‑CAGACGAGGTAATTCATCAATCATTTCCAAAAGCAACAATTATCTCTTTTACAAATTTATATCAGGCATTAGCa                                                    <  1:583668/98‑1 (MQ=255)

                                                                                                                        tGCTCGGGTAGCAAATTACCCCC‑C‑CAGACGAGGTAATTCATCAATCATTTCCAAAAGCAACAATTATCTCTTTTACAAATTTATATCAGGCATTAGCATCCGTCTCAGCTGGGCACAATGATTACTTTATTGGTAGTaa           >  1:265342/1‑139 (MQ=255)

                                                                                                                                 aGCAAATTACCCCC‑C‑CAGACGAGGTAATTCATCAATCATTTCCAAAAGCAACAATTATCTCTTTTACAAATTTATATCAGGCATTAGCATCCGTCTCAGCTGGGCACAATGATTACTTTATTGGTAGTAACATCATTAc  <  1:51069/139‑1 (MQ=255)

                                                                                                                                 aGCAAATTACCCCC‑C‑CAGACCAGGTAATTCATCAATCATTTCCAAAAGCAACAATTATCTCTTTTACAAATTTATATCAGGCATTAGCATCCGTCTCAGCTGGGCACAATGATTACTTTATTGGTAGTAACATCATTAc  <  1:149419/139‑1 (MQ=255)

TTCGCCGCCTCTTAATAATGACATTGCTGCAACCAAACCATTGATAATTACCTTTCCGGCGCTGGTAACCACCCTTCACGACTCAATGCGACCGCTTACCTCACCAAAACCAGTAAATATTGCTCGGGTAGCAAATTA‑CCCC‑C‑CAGACGAGGTAATTCATCAATCATTTCCAAAAGCAACAATTATCTCTTTTACAAATTTATATCAGGCATTAGCATCCGTCTCAGCTGGGCACAATGATTACTTTATTGGTAGTAACATCATTAC  >  NC_000913/2484754‑2485020

Alignment Legend
Aligned base mismatch/match (shaded by quality score): `ATCG/ATCG` `< 3 ≤` `ATCG/ATCG` `< 27 ≤` `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