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 I1 R1	759	65.2	3386260	90.7%	3071337	101.6

Breseq alignment

BRESEQ :: Evidence

Predicted mutation
evidence	seq id	position	mutation	annotation	gene	description
RA	NC_000913	1,204,160	G→A	113 (TAG→TAA)	ymfM →	e14 prophage, uncharacterized protein

Read alignment evidence...
	seq id	position		ref	new	freq	score (cons/poly)	reads	annotation	genes	product
*	NC_000913	1,204,160	0	G	A	97.4%	122.6 / ‑6.4	39	113 (TAG→TAA)	ymfM	e14 prophage, uncharacterized protein
Reads supporting (aligned to +/- strand): ref base G (0/0); major base A (16/22); minor base C (1/0); total (17/22)
Fisher's exact test for biased strand distribution p-value = 4.36e-01
Kolmogorov-Smirnov test that lower quality scores support variant p-value = 1.00e+00

AAGATCACTACGGAGTGCCCGTCAGAGTCATTCGTTGGGAGCCGGAAACACAACGGGTTATCTACCTCCGCGAAGGTTATGAGCATGAATGCTTCAGCCCGCTCGAACAGTTTCGTCGTAAATTCAGGGAAATAGAGGTCGGTCATGAGCACTAAATTAACCGGCTATGTATGGGATGGTTGCGCTGCATCAGGCATGAAGTTATCCAGCGTGGCAATTATGGCCCGCCTGGCTGATTTCAGTAATGACGAAGGT  >  NC_000913/1204026‑1204280

aaGATCACTACGGAGTGCCCGTCAGAGTCATTCGTTGGGAGCCGGAAACACAACGGGTTATCTACCTCCGCGAAGGTTATGAGCATGAATGCTTCAGCCCGCTCGAACAGTTTCGTCGTAAATTCAGGGAAATAAAggt                                                                                                                      <  1:834157/139‑1 (MQ=255)

       cTACGGAGTGCCCGTCAGAGTCATTCGTTGGGAGCCGGAAACACAACGGGTTATCTACCTCCGCGAAGGTTATGAGCATGAATGCTTCAGCCCGCTCGAACAGTTTCGTCGTAAATTCAGGGAAATAAAGGTCGGTCAt                                                                                                               <  1:218290/139‑1 (MQ=255)

        tACGGAGTGCCCGTCAGAGTCATTCGTTGGGAGCCGGAAACACAACGGGTTATCTACCTCCGCGAAGGTTATGAGCATGAATGCTTCAGCCCGCTCGAACAGTTTCGTCGTAAATTCAGGGAAATAAAGGTCGGTCATg                                                                                                              >  1:1447374/1‑139 (MQ=255)

                 cccGTCAGAGTCATTCGTTGGGAGCCGGAAACACAACGGGTTATCTACCTCCGCGAAGGTTATGAGCATGAATGCTTCAGCCCGCTCGAACAGTTTCGTCGTAAATTCAGGGAAATAAAggtcgg                                                                                                                   >  1:77597/1‑125 (MQ=255)

                 cccGTCAGAGTCATTCGTTGGGAGCCGGAAACACAACGGGTTATCTACCTCCGCGAAGGTTATGAGCATGAATGCTTCAGCCCGCTCGAACAGTTTCGTCGTAAATTCAGGGAAATAAAggtcgg                                                                                                                   <  2:77597/125‑1 (MQ=255)

                 cccGTCAGAGTCATTCGTTGGGAGCCGGAAACACAACGGGTTATCTACCTCCGCGAAGGTTATGAGCATGAATGCTTCAGCCCGCTCGAACAGTTTCGTCGTAAATTCAGGGAAATAAAGGTCGGTCATGAGCACTaaa                                                                                                     >  2:445051/1‑139 (MQ=255)

                      cAGAGTCATTCGTTGGGAGCCGGAAACACAACGGGTTATCTACCTCCGCGAAGGTTATGAGCATGAATGCTTCAGCCCGCTCGAACAGTTTCGTCGTAAATTCAGGGAAATAAAGGTCGGTCATGAGCACTAAATTAAc                                                                                                <  2:1019099/139‑1 (MQ=255)

                         agTCATTCGTTGGGAGCCGGAAACACAACGGGTTATCTACCTCCGCGAAGGTTATGAGCATGAATGCTTCAGCCCGCTCGAACAGTTTCGTCGTAAATTCAGGGAAATAAAGGTCGGTCATGAGCACTAAATTAAc                                                                                                <  1:137422/136‑1 (MQ=255)

                         agTCATTCGTTGGGAGCCGGAAACACAACGGGTTATCTACCTCCGCGAAGGTTATGAGCATGAATGCTTCAGCCCGCTCGAACAGTTTCGTCGTAAATTCAGGGAAATAAAGGTCGGTCATGAGCACTAAATTAAc                                                                                                >  2:137422/1‑136 (MQ=255)

                         agTCATTCGTTGGGAGCCGGAAACACAACGGGTTATCTACCTCCGCGAAGGTTATGAGCATGAATGCTTCAGCCCGCTCGAACAGTTTCGTCGTAAATTCAGGGAAATAAAGGTCGGTCATGAGCACTAAATTAACCgg                                                                                             <  2:1315824/139‑1 (MQ=255)

                           tCATTCGTTGGGAGCCGGAAACACAACGGGTTATCTACCTCCGCGAAGGTTATGAGCATGAATGCTTCAGCCCGCTCGAACAGTTTCGTCGTAAATTCAGGGAAATAAAGGTCGGTCATGAGCACTAAATTAACCGGCt                                                                                           <  1:1633341/139‑1 (MQ=255)

                                cGTTGGGAGCCGGAAACACAACGGGTTATCTACCTCCGCGAAGGTTATGAGCATGAATGCTTCAGCCCGCTCGAACAGTTTCGTCGTAAATTCAGGGAAATAAAGGTCGGTCATGAGCACTAAATTAACCGGCtatgta                                                                                      >  2:70159/1‑139 (MQ=255)

                                   tGGGAGCCGGAAACCCAACGGGTTATCTACCTCCGCGAAGGTTATGAGCATGAATGCTTCAGCCCGCTCGAACAGTTTCGTCGTAAATTCAGGGAAATACAGGTCGGTCATGAGCACTAAATTAACCGGc                                                                                            >  1:1026918/1‑130 (MQ=255)

                                   tGGGAGCCGGAAACACAACGGGTTATCTACCTCCGCGAAGGTTATGAGCATGAATGCTTCAGCCCGCTCGAACAGTTTCGTCGTAAATTCAGGGAAATAAAGGTCGGTCATGAGCACTAAATTAACCGGc                                                                                            <  2:1026918/130‑1 (MQ=255)

                                     ggAGCCGGAAACACAACGGGTTATCTACCTCCGCGAAGGTTATGAGCATGAATGCTTCAGCCCGCTCGAACAGTTTCGTCGTAAATTCAGGGAAATAAAGGTCGGTCATGAGCACTAAATTAACCGGCTATGTATGGGa                                                                                 >  2:1265290/1‑139 (MQ=255)

                                        gCCGGAAACACAACGGGTTATCTACCTCCGCGAAGGTTATGAGCATGAATGCTTCAGCCCGCTCGAACAGTTTCGTCGTAAATTCAGGGAAATAAAGGTCGGTCATGAGCACTAAATTAACCGGCTATGTATGGGATgg                                                                              <  1:70159/139‑1 (MQ=255)

                                         ccGGAAACACAACGGGTTATCTACCTCCGCGAAGGTTATGAGCATGAATGCTTCAGCCCGCTCGAACAGTTTCGTCGTAAATTCAGGGAAATAAAGGTCGGTCATGAGCACTAAATTAACCGGCTATGTATGGGATGGt                                                                             <  1:431454/139‑1 (MQ=255)

                                                   aaCGGGTTATCTACCTCCGCGAAGGTTATGAGCATGAATGCTTCAGCCCGCTCGAACAGTTTCGTCGTAAATTCAGGGAAATAAAGGTCGGTCATGAGCACTAAATTAACCGGCTATGTATGGGATGGTTGCGCTGCAt                                                                   <  2:1447374/139‑1 (MQ=255)

                                                      gggTTATCTACCTCCGCGAAGGTTATGAGCATGAATGCTTCAGCCCGCTCGAACAGTTTCGTCGTAAATTCAGGGAAATAAAGGTCGGTCAt                                                                                                               >  2:309933/1‑92 (MQ=255)

                                                      gggTTATCTACCTCCGCGAAGGTTATGAGCATGAATGCTTCAGCCCGCTCGAACAGTTTCGTCGTAAATTCAGGGAAATAAAGGTCGGTCAt                                                                                                               <  1:309933/92‑1 (MQ=255)

                                                                 cTCCGCGAAGGTTATGAGCATGAATGCTTCAGCCCGCTCGAACAGTTTCGTCGTAAATTCAGGGAAATAAAGGTCGGTCATGAGCACTAAATTAACCGGCTATGTATGGGATGGTTGCGCTGCATCAGGCATGAAGTTa                                                     >  1:1549707/1‑139 (MQ=255)

                                                                    cgcgAAGGTTATGAGCATGAATGCTTCAGCCCGCTCGAACAGTTTCGTCGTAAATTCAGGGAAATAAAggtcg                                                                                                                    >  1:263483/1‑73 (MQ=255)

                                                                    cgcgAAGGTTATGAGCATGAATGCTTCAGCCCGCTCGAACAGTTTCGTCGTAAATTCAGGGAAATAAAggtcg                                                                                                                    <  2:263483/73‑1 (MQ=255)

                                                                      cgAAGGTTATGAGCATGAATGCTTCAGCCCGCTCGAACAGTTTCGTCGTAAATTCAGGGAAATAAAGGTCGGTCATGAGCACTAAATTAACCgg                                                                                             >  2:536641/1‑94 (MQ=255)

                                                                      cgAAGGTTATGAGCATGAATGCTTCAGCCCGCTCGAACAGTTTCGTCGTAAATTCAGGGAAATAAAGGTCGGTCATGAGCACTAAATTAACCgg                                                                                             <  1:536641/94‑1 (MQ=255)

                                                                      cgAAGGTTATGAGCATGAATGCTTCAGCCCGCTCGAACAGTTTCGTCGTAAATTCAGGGAAATAAAGGTCGGTCATGAGCACTAAATTAACCGGCTATGTATGGGATGGTTGCGCTGCATCAGGCATGAAGTTATCCAg                                                <  2:1549707/139‑1 (MQ=255)

                                                                           gTTATGAGCATGAATGCTTCAGCCCGCTCGAACAGTTTCGTCGTAAATTCAGGGAAATAAAGGTCGGTCATGAGCACTAAATTAACCGGCTATGTATGGGATGGTTGCGCTGCATCAGGCATGAAGTTATCCAGCGTgg                                           >  1:705091/1‑139 (MQ=255)

                                                                                   cATGAATGCTTCAGCCCGCTCGAACAGTTTCGTCGTAAATTCAGGGAAATAAAGGTCGGTCATGAGCACTAAATTAACCGGCTATGTATGGGATGGTTGCGCTGCATCAGGCATGAAGTTATCCAGCGTGGCAATTATg                                   <  1:1265290/139‑1 (MQ=255)

                                                                                     tGAATGCTTCAGCCCGCTCGAACAGTTTCGTCGTAAATTCAGGGAAATAAAGGTCGGTCAt                                                                                                               >  1:43513/1‑61 (MQ=255)

                                                                                     tGAATGCTTCAGCCCGCTCGAACAGTTTCGTCGTAAATTCAGGGAAATAAAGGTCGGTCAt                                                                                                               <  2:43513/61‑1 (MQ=255)

                                                                                     tGAATGCTTCAGCCCGCTCGAACAGTTTCGTCGTAAATTCAGGGAAATAAAGGTCGGTCATGAGCACTAAATTAACCGGCTATGTATGGGATGGTTGCGCTGCATCAGGCATGAAGTTATCCAGCGTGGCAATTATGGc                                 >  2:1342116/1‑139 (MQ=255)

                                                                                        aTGCTTCAGCCCGCTCGAACAGTTTCGTCGTAAATTCAGGGAAATAAAGGTCGGTCATGAGCACTAAATTAACCGGCTATGTATGGGATGGTTGCGCTGCATCAGGCATGAAGTTATCCAGCGTGGCAATTATGGCCCg                              <  1:445051/139‑1 (MQ=255)

                                                                                                     cTCGAACAGTTTCGTCGTAAATTCAGGGAAATAAAGGTCGGTCATGAGCACTAAATTAACCGGCTATGTATGGGATGGTTGCGCTGCATCAGGCATGAAGTTATCCAGCGTGGCAATTATGGCCCGCCTGGCTGATTTc                 >  2:681154/1‑139 (MQ=255)

                                                                                                     cTCGAACAGTTTCGTCGTAAATTCAGGGAAATAAAGGTCGGTCATGAGCACTAAATTAACCGGCTATGTATGGGATGGTTGCGCTGCATCAGGCATGAAGTTATCCAGCGTGGCAATTATGGCCCGCCTGGCTGATTTc                 >  1:1436041/1‑139 (MQ=255)

                                                                                                        gAACAGTTTCGTCGTAAATTCAGGGAAATAAAGGTCGGTCATGAGCACTAAATTAACCGGCTATGTATGGGATGGTTGCGCTGCATCAGGCATGAAGTTATCCAGCGTGGCAATTATGGCCCGCCTGGCTGATTTCAGt              <  1:1342116/139‑1 (MQ=255)

                                                                                                               ttCGTCGTAAATTCAGGGAAATAAAGGTCGGTCATGAGCACTAAATTAACCGGCTATGTATGGGATGGTTGCGCTGCATCAGGCATGAAGTTATCCAGCGTGGCAATTATGGCCCGCCTGGCTGATTTCAGTAATGACg       <  1:681154/139‑1 (MQ=255)

                                                                                                                tcgtcgTAAATTCAGGGAAATAAAGGTCGGTCATGAGCACTAAATTAACCGGCTATGTATGGGATGGTTGCGCTGCATCAGGCATGAAGTTATCCAGCGTGGCAATTATg                                   >  2:308205/1‑110 (MQ=255)

                                                                                                                tcgtcgTAAATTCAGGGAAATAAAGGTCGGTCATGAGCACTAAATTAACCGGCTATGTATGGGATGGTTGCGCTGCATCAGGCATGAAGTTATCCAGCGTGGCAATTATg                                   <  1:308205/110‑1 (MQ=255)

                                                                                                                    cgtAAATTCAGGGAAATAAAGGTCGGTCATGAGCACTAAATTAACCGGCTATGTATGGGATGGTTGCGCTGCATCAGGCATGAAGTTATCCAGCGTGGCAATTATGGCCCGCCTGGCTGATTTCAGTAATGACGAAGgt  <  2:753088/139‑1 (MQ=255)

AAGATCACTACGGAGTGCCCGTCAGAGTCATTCGTTGGGAGCCGGAAACACAACGGGTTATCTACCTCCGCGAAGGTTATGAGCATGAATGCTTCAGCCCGCTCGAACAGTTTCGTCGTAAATTCAGGGAAATAGAGGTCGGTCATGAGCACTAAATTAACCGGCTATGTATGGGATGGTTGCGCTGCATCAGGCATGAAGTTATCCAGCGTGGCAATTATGGCCCGCCTGGCTGATTTCAGTAATGACGAAGGT  >  NC_000913/1204026‑1204280

Alignment Legend
Aligned base mismatch/match (shaded by quality score): `ATCG/ATCG` `< 3 ≤` `ATCG/ATCG` `< 30 ≤` `ATCG/ATCG` `< 35 ≤` `ATCG/ATCG` `< 39 ≤` `ATCG/ATCG` `< 40 ≤` `ATCG/ATCG`
Unaligned base: `atcg` Masked matching base: `atcg` Alignment gap: `‑` Deleted base: `‑`

GATK/CNVnator alignment

N/A