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
A21 F117 I1 R2	26	38.4	896262	90.9%	814702	136.0

Breseq alignment

BRESEQ :: Evidence

Predicted mutation
evidence	seq id	position	mutation	annotation	gene	description
RA	CP000730	2,679,803	G→T	G96V (GGA→GTA)	cbpD →	possible secretory antigen

Read alignment evidence...
	seq id	position		ref	new	freq	score (cons/poly)	reads	annotation	genes	product
*	CP000730	2,679,803	0	G	T	97.3%	113.7 / ‑4.8	37	G96V (GGA→GTA)	cbpD	possible secretory antigen
Reads supporting (aligned to +/- strand): ref base G (0/1); new base T (17/19); total (17/20)
Fisher's exact test for biased strand distribution p-value = 1.00e+00
Kolmogorov-Smirnov test that lower quality scores support variant p-value = 9.63e-01

CGTCGCGCACAAGTCGGTAAACCTGTTTCTAATAGATGGGGCAATGCTAAAAATTGGTATTACAATGCACGTAAATCAAAATATGCGACTGGTCGTACACCAAGAAAATTTGCTGTCATGCAATCAACTGCAGGATATTATGGACATGTCGCAGTTGTTGAACAAGTATATAAAAACGGTAGTATTAAAGTTTCAGAATACAACTTTTATCGCCCATTAAAATACAATACACGTGTACTAAGCAAAAAGGCAGCACGTAACTTTAACT  >  CP000730/2679670‑2679937

cGTCGCGCACAAGTCGGTAAACCTGTTTCTAATAGATGGGGCAATGCTAAAAATTGGTATTACAATGCACGTAAATCAAAATATGCGACTGGTCGTACACCAAGAAAATTTGCTGTCATGCAATCAACTGCAGTAtattat                                                                                                                                 >  2:48865/1‑141 (MQ=255)

     cgcACAAGTCGGTAAACCTGTTTCTAATAGATGGGGCAATGCTAAAAATTGGTATTACAATGCACGTAAATCAAAATATGCGACTGGTCGTACACCAAGAAAATTTGCTGTCATGCAATCAACTGCAGGATATTATGGACa                                                                                                                            <  2:300334/141‑1 (MQ=255)

      gcACAAGTCGGTAAACCTGTTTCTAATAGATGGGGCAATGCTAAAAATTGGTATTACAATGCACGTAAATCAAAATATGCGACTGGTCGTACACCAAGAAAATTTGCTGTCATGCAATCAACTGCAGTATATTATGGACAt                                                                                                                           >  1:420858/1‑141 (MQ=255)

           aGTCGGTAAACCTGTTTCTAATAGATGGGGCAATGCTAAAAATTGGTATTACAATGCACGTAAATCAAAATATGCGACTGGTCGTACACCAAGAAAATTTGCTGTCATGCAATCAACTGCAGTATATTATGGACATGTCGc                                                                                                                      <  1:86976/141‑1 (MQ=255)

            gTCGGTAAACCTGTTTCTAATAGATGGGGCAATGCTAAAAATTGGTATTACAATGCACGTAAATCAAAATATGCGACTGGTCGTACACCAAGAAAATTTGCTGTCATGCAATCAACTGCAGTATATTATGGACATGTCGCa                                                                                                                     >  2:120829/1‑141 (MQ=255)

               ggTAAACCTGTTTCTAATAGATGGGGCAATGCTAAAAATTGGTATTACAATGCACGTAAATCAAAATATGCGACTGGTCGTACACCAAGAAAATTTGCTGTCATGCAATCAACTGCAGTATATTATGGACATGTCGCAgtt                                                                                                                  <  1:147117/141‑1 (MQ=255)

                gTAAACCTGTTTCTAATAGATGGGGCAATGCTAAAAATTGGTATTACAATGCACGTAAATCAAAATATGCGACTGGTCGTACACCAAGAAAATTTGCTGTCATGCAATCAACTGCAGTATATTATGGACATGTCGCAgttg                                                                                                                 >  2:58024/1‑141 (MQ=255)

                  aaaCCTGTTTCTAATAGATGGGGCAATGCTAAAAATTGGTATTACAATGCACGTAAATCAAAATATGCGACTGGTCGTACACCAAGAAAATTTGCTGTCATGCAATCAACTGCAGTATATTATGGACATGTCGCAgttgtt                                                                                                               <  1:222923/141‑1 (MQ=255)

                        gTTTCTAATAGATGGGGCAATGCTAAAAATTGGTATTACAATGCACGTAAATCAAAATATGCGACTGGTCGTACACCAAGAAAATTTGCTGTCATGCAATCAACTGCAGTATATTATGGACATGTCGCAGTTGTTGAACaa                                                                                                         >  1:9209/1‑141 (MQ=255)

                            cTAATAGATGGGGCAATGCTAAAAATTGGTATTACAATGCACGTAAATCAAAATATGCGACTGGTCGTACACCAAGAAAATTTGCTGTCATGCAATCAACTGCAGTATATTATGGACATGTCGCAGTTGTTGAACAAGtat                                                                                                     <  1:120829/141‑1 (MQ=255)

                               agagagGGGGGAGTGCTAAGAAGTGGGAGTACGATGCAGGTAGATCAAAATATGCGACTGGTCGTACACCAAGGAAATGTGGTGGCATGCAATCAACTGCAGTATATGGTGGACATGTCGCAGTTGTTGAACAAGtatata                                                                                                  <  2:399796/139‑1 (MQ=255)

                                      gggCAATGCTAAAAATTGGTATTACAATGCACGTAAATCAAAATATGCGACTGGTCGTACACCAAGAAAATTTGCTGTCATGCAATCAACTGCAGTATATTATGGACATGTCGCAGTTGTTGAACAAGTATATAAAAACgg                                                                                           <  1:160814/141‑1 (MQ=255)

                                      gggCAATGCTAAAAATTGGTATTACAATGCACGTAAATCAAAATATGCGACTGGTCGTACACCAAGAAAATTTGCTGTCATGCAATCAACTGCAGTATATTATGGACATGTCGCAGTTGTTGAACAAGTATATAAAAACgg                                                                                           >  1:358015/1‑141 (MQ=255)

                                        gCAATGCTAAAAATTGGTATTACAATGCACGTAAATCAAAATATGCGACTGGTCGTACACCAAGAAAATTTGCTGTCATGCAATCAACTGCAGTATATTATGGACATGTCGCAGTTGTTGAACAAGTATATAAAAACGgta                                                                                         <  2:247861/141‑1 (MQ=255)

                                            tGCTAAAAATTGGTATTAAAATGAAAGTAAATCAAAATATGCGACTGGTCGTACACCAAGAAAATTTGCTGTCATGCAATCAACTGCAGTATATTATGGACATGTCGCAGTTGTTGAAAAAAAATATAAAAACGGTAGTAt                                                                                     <  2:9209/141‑1 (MQ=255)

                                             gCTAAAAATTGGTATTACAATGCACGTAAATCAAAATATGCGACTGGTCGTACACCAAGAAAATTTGCTGTCATGCAATCAACTGCAGTATATTATGGACATGTCGCAGTTGTTGAACAAGTATATAAAAACGGTAGTAtt                                                                                    <  1:194781/141‑1 (MQ=255)

                                             gCTAAAAATTGGTATTACAATGCACGTAAATCAAAATATGCGACTGGTCGTACACCAAGAAAATTTGCTGTCATGCAATCAACTGCAGTATATTATGGACATGTCGCAGTTGTTGAACAAGTATATAAAAACGGTAGTAtt                                                                                    <  1:162889/141‑1 (MQ=255)

                                                 aaaaTTGGTATTACAATGCACGTAAATCAAAATATGCGACTGGTCGTACACCAAGAAAATTTGCTGTCATGCAATCAACTGCAGTATATTATGGACATGTCGCAGTTGTTGAACAAGTATATAAAAACGGTAGTATTAAAg                                                                                <  1:244768/141‑1 (MQ=255)

                                                       ggTATTACAATGCACGTAAATCAAAATATGCGACTGGTCGTACACCAAGAAAATTTGCTGTCATGCAATCAACTGCAGTATATTATGGACATGTCGCAGTTGTTGAACAAGTATATAAAAACGGTAGTATTAAAGTTTCAg                                                                          <  1:330117/141‑1 (MQ=255)

                                                        gTATTNCAATGCACGTAAATCAAAATATGCGACTGGTCGTACACCAAGAAAATTTGCTGTGATGCAATCAACTGCAGTATATTATGGACATGTCGCAGTTGTTGAACAAGTATATAAAAACGGTAGTATTAAAGTTTCAGa                                                                         <  1:118460/141‑1 (MQ=255)

                                                             aCAATGCACGTAAATCAAAATATGCGACTGGTCGTACACTAAGAAAAATTGCTGTCATGCAATCAACTGCAGTATATTATGGACATGTCGCAGTTGTTGAACAAGTCTCTACAAACGGTAATATTAAAGTATCCGCATACa                                                                    >  2:342609/1‑141 (MQ=255)

                                                              cAATGCACGTAAATCAAAATATGCGACTGGTCGTACACCCAGAAAATTAGCTGTCATGCAATCAACTGCAGTATATTATGGACATGTCGCAGTTGTTGAACAAGTATATAACAACGGTAGTATCAAAGTCACAGAATACaa                                                                   >  2:263925/1‑141 (MQ=255)

                                                                 tGCACGTAAATCAAAATATGCGACTGGTCGTACACCAAGAAAATTTGCTGTCATGCAATCAACTGCAGTATATTATGGACATGTCGCAGTTGTTGAACAAGTATATAAAAACGGTAGTATTAAAGTTTCAGAATACAACtt                                                                >  2:174011/1‑141 (MQ=255)

                                                                  gCACGTAAATCAAAATATGCGACTGGTCGTACACCAAGAAAATTTGCTGTCATGCAATCAACTGCAGTATATTATGGACATGTCGCAGTTGTTGAACAAGTATATAAAAACGGTAGTATTAAAGTTTCAGAATACAACttt                                                               >  1:295894/1‑141 (MQ=255)

                                                                     cGTAAATCAAAATATGCGACTGGTCGTACACCAAGAAAATTTGCTGTCATGCAATCAACTGCAGTATATTATGGACATGTCGCAGTTGTTGAACAAGTATATAAAAACGGTAGTATTAAAGTTTCAGAATACAACTTTTAt                                                            >  2:224425/1‑141 (MQ=255)

                                                                          aTCAAAATATGCGACTGGTCGTACACCAAGAAAATTTGCTGTCATGCAATCAACTGCAGTATATTATGGACATGTCGCAGTTGTTGAACAAGTATATAAAAACGGTAGTATTAAAGTTTCAGAATACAACTTTTATCGccc                                                       >  1:407632/1‑141 (MQ=255)

                                                                            cAAAATATGCGACTGGTCGTACACCAAGAAAATTTGCTGTCATGCAATCAACTGCAGTATATTATGGACATGTCGCAGTTGTTGAACAAGTATATAAAAACGGTAGTATTAAAGTTTCAGAATACAACTTTTATCGCCCAt                                                     <  1:305385/141‑1 (MQ=255)

                                                                            cAAAATATGCGACTGGTCGTACACCAAGAAAATTTGCTGTCATGCAATCAACTGCAGTATATTATGGACATGTCGCAGTTGTTGAACAAGTATATAAAAACGGTAGTATTAAAGTTTCAGAATACAACTTTTATCGCCCAt                                                     <  2:257407/141‑1 (MQ=255)

                                                                                            tCGTACACCAAGAAAATTTGCTGTCATGCAATCAACTGCAGTATATTATGGACATGTCGCAGTTGTTGAACAAGTATATAAAAACGGTAGTATTAAAGTTTCAGAATACAACTTTTATCGCCCATTAAAATACAATACACg                                     <  1:58024/141‑1 (MQ=255)

                                                                                                 caacAAGAAAAATTGCTAGCAAGAAAGCAACTGAAATATATTATGGAAATATCGCAGTTGTTGAAAAAGTATATAAAAACGGAAGTATTAAAGTTTCAGAATACAAATTTTATCGCCCATTAACATTCAATACACgaataa                                <  2:341279/138‑6 (MQ=255)

                                                                                                    cAAGAAAATTTGCTGTCATGCAATCAACTGCAGTATATTATGGACATGTCGCAGTTGTTGAACAAGTATATAAAAACGGTAGTATTAAAGTTTCAGAATACAACTTTTATCGCCCATTAAAATACAATACACGTGTACTaa                             >  1:40685/1‑141 (MQ=255)

                                                                                                    cAAGAAAATTTGCTGTCATGCAATCAACTGCAGTATATTAAGGACATGTCGCAGTTGTTGAACAAGTATATAAAAACGGAAGTATTAAAGTTTCAGAATACAACTTTTATCGCCCATTAAAATACAATACACGTGTACTaa                             >  2:59768/1‑141 (MQ=255)

                                                                                                           aTTTGCTGTCATGCAATCAACTGCAGTATATTATGGACATGTCGCAGTTGTTGAACAAGTATATAAAAACGGTAGTATTAAAGTTTCAGAATACAACTTTTATCGCCCATTAAAATACAATACACGTGTACTAAGCaaaaa                      >  1:171508/1‑141 (MQ=255)

                                                                                                                cTGTCATGCAATCAACTGCAGTATATTATGGACATGTCGCAGTTGTTGAACAAGTATATAAAAACGGTAGTATTAAAGTTTCAGAATACAACTTTTATCGCCCATTAAAATACAATACACGTGTACTAAGCAAAAAGgcag                 >  1:66766/1‑141 (MQ=255)

                                                                                                                  gTCATGCAATCAACTGCAGTATATTATGGACATGTCGCAGTTGTTGAACAAGTATATAAAAACGGTAGTATTAAAGTTTCAGAATACAACTTTTATCGCCCATTAAAATACAATACACGTGTACTAAGCAAAAAGgcagca               <  1:305591/141‑1 (MQ=255)

                                                                                                                           tCAACTGCAGTATATTATGGACATGTCGCAGTTGTTGAACAAGTATATAAAAACGGTAGTATTAAAGTTTCAGAATACAACTTTTATCGCCCATTAAAATACAATACACGTGTACTAAGCAAAAAGGCAGCACGTAACttt      <  2:295894/141‑1 (MQ=255)

                                                                                                                               cTGCAGTATATTATGGACATGTCGCAGTTGTTGAACAAGTATATAAAAACGGTAGTATTAAAGTTTCAGAATACAACTTTTATCGCCCATTAAAATACAATACACGTGTACTAAGCAAAAAGGCAGCACGTAACTTTAACt  >  2:267628/1‑141 (MQ=255)

CGTCGCGCACAAGTCGGTAAACCTGTTTCTAATAGATGGGGCAATGCTAAAAATTGGTATTACAATGCACGTAAATCAAAATATGCGACTGGTCGTACACCAAGAAAATTTGCTGTCATGCAATCAACTGCAGGATATTATGGACATGTCGCAGTTGTTGAACAAGTATATAAAAACGGTAGTATTAAAGTTTCAGAATACAACTTTTATCGCCCATTAAAATACAATACACGTGTACTAAGCAAAAAGGCAGCACGTAACTTTAACT  >  CP000730/2679670‑2679937

Alignment Legend
Aligned base mismatch/match (shaded by quality score): `ATCG/ATCG` `< 3 ≤` `ATCG/ATCG` `< 12 ≤` `ATCG/ATCG` `< 27 ≤` `ATCG/ATCG` `< 41 ≤` `ATCG/ATCG`
Unaligned base: `atcg` Masked matching base: `atcg` Alignment gap: `‑` Deleted base: `‑`

GATK/CNVnator alignment

N/A