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
A4 F1 I1 R1	765	39.6	1867486	94.4%	1762906	108.0

Breseq alignment

BRESEQ :: Evidence

Predicted mutation
evidence	seq id	position	mutation	annotation	gene	description
RA	NC_000913	1,942,993	G→A	G111E (GGG→GAG)	znuC →	zinc ABC transporter ATPase

Read alignment evidence...
	seq id	position		ref	new	freq	score (cons/poly)	reads	annotation	genes	product
*	NC_000913	1,942,993	0	G	A	96.5%	171.0 / ‑1.8	58	G111E (GGG→GAG)	znuC	zinc ABC transporter ATPase
Reads supporting (aligned to +/- strand): ref base G (1/1); new base A (28/28); total (29/29)
Fisher's exact test for biased strand distribution p-value = 1.00e+00
Kolmogorov-Smirnov test that lower quality scores support variant p-value = 2.21e-01

CGCATCGGCTATGTACCGCAGAAGCTGTATCTCGACACCACGTTGCCACTGACCGTAAACCGTTTTTTACGCTTACGCCCTGGTACACATAAAGAAGATATTTTGCCTGCACTGAAACGTGTCCAGGCCGGGCACCTGATTAACGCACCGATGCAAAAGCTCTCTGGTGGCGAAACGCAGCGTGTACTATTAGCGCGAGCATTGTTAAATCGCCCGCAATTATTAGTGCTGGATGAACCCACTCAAGGCGTGGATGTAAATGGC  >  NC_000913/1942863‑1943126

cgcATCGGCTATGTACCGCAGAAGCTGTATCTCGACACCACGTTGCCACTGACCGTAAACCGTTTTTTACGCTTACGCCCTGGTACACATAAAGAAGATATTTTGCCTGCACTGAAACGTGTCCAGGCCGAGCACCTGa                                                                                                                               >  1:121812/1‑139 (MQ=255)

  cATCGGCTATGTACCGCAGAAGCTGTATCTCGACACCACGTTGCCACTGACCGTAAACCGTTTTTTACGCTTACGCCCTGGTACACATAAAGAAGATATTTTGCCTGCACTGAAACGTGTCCAGGCCGAGCACCTGAtt                                                                                                                             >  2:129610/1‑139 (MQ=255)

    tCGGCTATGTACCGCAGAAGCTGTATCTCGACACCACGTTGCCACTGACCGTAAACCGTTTTTTACGCTTACGCCCTGGTACACATAAAGAAGATATTTTGCCTGCACTGAAACGTGTCCAGGCCGAGCACCTGATTaa                                                                                                                           <  2:932680/139‑1 (MQ=255)

      ggCTATGTACCGCAGAAGCTGTATCTCGACACCACGTTGCCACTGACCGTAAACCGTTTTTTACGCTTACGCCCTGGTACACATAAAGAAGATATTTTGCCTGCACTGAAACGTGTCCAGGCCGAGCACCTGATTAACg                                                                                                                         <  2:305360/139‑1 (MQ=255)

                 gCAGAAGCTGTATCTCGACACCACGTTGCCACTGACCGTAAACCGTTTTTTACGCTTACGCCCTGGTACACATAAAGAAGATATTTTGCCTGCACTGAAACGTGTCCAGGCCGAGCACCTGATTAACGCACCGATGCaa                                                                                                              <  1:285596/139‑1 (MQ=255)

                     aaGCTGTATCTCGACACCACGTTGCCACTGACCGTAAACCGTTTTTTACGCTTACGCCCTGGTACACATAAAGAAGATATTTTGCCTGCACTGAAACGTGTCCAGGCCGAGCACCTGATTAACGCACCGATGCAAAAGc                                                                                                          >  2:731693/1‑139 (MQ=255)

                     aaGCTGTATCTCGACACCACGTTGCCACTGACCGTAAACCGTTTTTTACGCTTACGCCCTGGTACACATAAAGAAGATATTTTGCCTGCACTGAAACGTGTCCAGGCCGAGCACCTGATTAACGCACCGATGCAAAAGc                                                                                                          >  2:528505/1‑139 (MQ=255)

                     aaGCTGTATCTCGACACCACGTTGCCACTGACCGTAAACCGTTTTTTACGCTTACGCCCTGGTACACATAAAGAAGATATTTTGCCTGCACTGAAACGTGTCCAGGCCGAGCACCTGATTAACGCACCGATGCAAAAGc                                                                                                          >  1:442681/1‑139 (MQ=255)

                      aGCTGTATCTCGACACCACGTTGCCACTGACCGTAAACCGTTTTTTACGCTTACGCCCTGGTACACATAAAGAAGATATTTTGCCTGCACTGAAACGTGTCCAGGCCGAGCACCTGATTAACGCACCGATGCAAAAGct                                                                                                         <  1:528505/139‑1 (MQ=255)

                                        cGTTGCCACTGACCGTAAACCGTTTTTTACGCTTACGCCCTGGTACACATAAAGAAGATATTTTGCCTGCACTGAAACGTGTCCAGGCCGAGCACCTGATTAACGCACCGATGCAAAAGCTCTCTGGTGGCGAAACGCa                                                                                       <  1:79713/139‑1 (MQ=255)

                                         gTTGCCACTGACCGTAAACCGTTTTTTACGCTTACGCCCTGGTACACATAAAGAAGATATTTTGCCTGCACTGAAACGTGTCCAGGCCGAGCACCTGATTAACGCACCGATGCAAAAGCTCTCTGGTGGCGAAACGCAg                                                                                      <  2:480970/139‑1 (MQ=255)

                                           tGCCACTGACCGTAAACCGTTTTTTACGCTTACGCCCTGGTACACATAAAGAAGATATTTTGCCTGCACTGAAACGTGTCCAGGCCGAGCACCTGATTAACGCACCGATGCaa                                                                                                              <  1:291871/113‑1 (MQ=255)

                                           tGCCACTGACCGTAAACCGTTTTTTACGCTTACGCCCTGGTACACATAAAGAAGATATTTTGCCTGCACTGAAACGTGTCCAGGCCGAGCACCTGATTAACGCACCGATGCaa                                                                                                              >  2:291871/1‑113 (MQ=255)

                                             ccACTGACCGTAAACCGTTTTTTACGCTTACGCCCTGGTACACATAAAGAAGATATTTTGCCTGCACTGAAACGTGTCCAGGCCGAGCACCTGATTAACGCACCGATGCAAAAGCTCTCTGGTGGCGAAACGCAGCgtg                                                                                  <  2:214736/139‑1 (MQ=255)

                                                            cGTTTTTTACGCTTACGCCCTGGTACACATAAAGAAGATATTTTGCCTGCACTGAAACGTGTCCAGGCCGAGCACCTGATTAACGCACCGATGCAAAAGCTCTCTGGTGGCGAAACGCAGCGTGTACTATTAGCGCGAg                                                                   <  2:118283/139‑1 (MQ=255)

                                                            cGTTTTTTACGCTTACGCCCTGGTACACATAAAGAAGATATTTTGCCTGCACTGAAACGTGTCCAGGCCGAGCACCTGATTAACGCACCGATGCAAAAGCTCTCTGGTGGCGAAACGCAGCGTGTACTATTAGCGCGAg                                                                   <  1:323742/139‑1 (MQ=255)

                                                              ttttttACGCTTACGCCCTGGTACACATAAAGAAGATATTTTGCCTGCACTGAAACGTGTCCAGGCCGAGCACCTGATTAACGCACCGATGCAAAAGCTCTCTGGTGGCGAAACGCAGCg                                                                                    >  1:587740/1‑120 (MQ=255)

                                                              ttttttACGCTTACGCCCTGGTACACATAAAGAAGATATTTTACCTGCACTGAAACGTGTCCAGGCCGAGCACCTGATTAACGCACCGATGCAAAAGCTCTCTGGTGGCGAAACGCAGcc                                                                                    <  2:587740/120‑2 (MQ=255)

                                                               tttttACGCTTACGCCCTGGTACACATAAAGAAGATATTTTGCCTGCACTGAAACGTGTCCAGGCCGAGCACCTGATTAACGCACCGATGCAAAAGCTCTCTGGTGGCGAAACGCAGCgtg                                                                                  <  1:547190/121‑1 (MQ=255)

                                                               tttttACGCTTACGCCCTGGTACACATAAAGAAGATATTTTGCCTGCACTGAAACGTGTCCAGGCCGAGCACCTGATTAACGCACCGATGCAAAAGCTCTCTGGTGGCGAAACGCAGCgtg                                                                                  >  2:547190/1‑121 (MQ=255)

                                                                            gcCCTGGTACACATAAAGAAGATATTTTGCCTGCACTGAAACGTGTCCAGGCCGAGCACCTGATTAACGCACCGATGCAAAAGCTCTCTGGTGGCGAAACGCAGCGTGTACTATTAGCGCGAGCATTGTTAAATCGccc                                                   <  1:129610/139‑1 (MQ=255)

                                                                                tGGTACACATAAAGAAGATATTTTGCCTGCACTGAAACGTGTCCAGGCCGAGCACCTGATTAACGCACCGATGCAAAAGCTCTCTGGTGGCGAAACGCAGCGTGTACTATTAGCGCGAg                                                                   <  2:781716/119‑1 (MQ=255)

                                                                                tGGTACACATAAAGAAGATATTTTGCCTGCACTGAAACGTGTCCAGGCCGAGCACCTGATTAACGCACCCATGCAAAAGCTCTCTAGTGGCGAAACGCAGCGTGTACCATTAGCGCGAg                                                                   >  1:781716/1‑119 (MQ=255)

                                                                                  gTACACATAAAGAAGATATTTTGCCTGCACTGAAACGTGTCCAGGCCGAGCACCTGATTAACGCACCGATGCAAAAGCTCTCTGGTGGCGAAACGCAGCGTGTACTATTAGCGCGAGCATTGTTaaa                                                         <  1:498969/127‑1 (MQ=255)

                                                                                  gTACACATAAAGAAGATATTTTGCCTGCACTGAAACGTGTCCAGGCCGAGCACCTGATTAACGCACCGATGCAAAAGCTCTCTGGTGGCGAAACGCAGCGTGTACTATTAGCGCGAGCATTGTTaaa                                                         >  2:498969/1‑127 (MQ=255)

                                                                                        aTAAAGAAGATATTTTGCCTGCACTTAAACGTGTCCAGGCCGAGCACCTGATTAACGCACCGATGCAATAGCTCTCTGGTGGCGAAACGCAGCGTGTACTATTAGCGCGATCATTTTTAAATCGCCCGCAattataaat                                       >  2:466656/1‑135 (MQ=255)

                                                                                        aTAAAGAAGATATTTTGCCTGCACTGAAACGTGTCCAGGCCGAGCACCTGATTAACGCACCGATGCAAAAGCTCTCTGGTGGCGAAACGc                                                                                        >  2:226984/1‑90 (MQ=255)

                                                                                        aTAAAGAAGATATTTTGCCTGCACTGAAACGTGTCCAGGCCGAGCACCTGATTAACGCACCGATGCAAAAGCTCTCTGGTGGCGAAACGc                                                                                        <  1:226984/90‑1 (MQ=255)

                                                                                        aTAAAGAAGATATTTTGCCTGCACTGAAACGTGTCCAGGCCGAGCACCTGATTAACGCACCGATGCAAAAGCTCTCTGGTGGCGAAACGCa                                                                                       >  2:307202/1‑91 (MQ=255)

                                                                                        aTAAAGAAGATATTTTGCCTGCACTGAAACGTGTCCAGGCCGAGCACCTGATTAACGCACCGATGCAAAAGCTCTCTGGTGGCGAAACGCa                                                                                       <  1:307202/91‑1 (MQ=255)

                                                                                        aTAAAGAAGATATTTTGCCTGCACTGAAACGTGTCCAGGCCGAGCACCTGATTAACGCACCGATGCAAAAGCTCTCTGGTGGCGAAACGCAg                                                                                      <  1:507414/92‑1 (MQ=255)

                                                                                        aTAAAGAAGATATTTTGCCTGCACTGAAACGTGTCCAGGCCGAGCACCTGATTAACGCACCGATGCAAAAGCTCTCTGGTGGCGAAACGCAg                                                                                      >  2:507414/1‑92 (MQ=255)

                                                                                        aTAAAGAAGATATTTTGCCTGCACTGAAACGTGTCCAGGCCGAGCACCTGATTAACGCACCGATGCAAAAGCTCTCTGGTGGCGAAACGCAGCGTGTACTATTAGCGCGAGCATTGTTAAATCGCCCGCAATTATTAGt                                       >  2:427472/1‑139 (MQ=255)

                                                                                        aTAAAGAAGATATTTTGCCTGCACTGAAACGTGTCCAGGCCGAGCACCTGATTAACGCACCGATGCAAAAGCTCTCTGGTGGCGAAACGCAGCGTGTACTATTAGCGCGAGCATTGTTAAATCGCCCGCAATTATTAGt                                       >  1:241222/1‑139 (MQ=255)

                                                                                        aTAAAGAAGATATTTTGCCTGCACTGAAACGTGTCCAGGCC‑GGCACCTGATTAACGCACCGATGCAAAAGCTCTCTGGTGGCGa                                                                                             <  1:12655/84‑1 (MQ=255)

                                                                                        aTAAAGAAGATATTTTGCCTGCACTGAAACGTGTCCAGGCC‑GGCACCTGATTAACGCACCGATGCAAAAGCTCTCTGGTGGCGa                                                                                             >  2:12655/1‑84 (MQ=255)

                                                                                            agaagaTATTTTGCCTGCACTGAAACGTGTCCAGGCCGAGCACCt                                                                                                                                 <  2:749798/45‑1 (MQ=255)

                                                                                            agaagaTATTTTGCCTGCACTGAAACGTGTCCAGGCCGAGCACCt                                                                                                                                 >  1:749798/1‑45 (MQ=255)

                                                                                            agaagaTATTTTGCCTGCACTGAAACGTGTCCAGGCCGAGCACCTGATTAACGCACCGATGCAAAAGCTCTCTGGTGGCGAAACGCAGCGTGTACTATTAGCGCGAGCATTGTTAAATCGCCCGCAATTATTAGTGCTg                                   >  1:818825/1‑139 (MQ=255)

                                                                                                gaTATTTTGCCTGCACTGAAACGTGTCCGGGCCGAGCACCTGATTAACGCACCGATGCAAAAGCTCTCTGGTGGCGAAACGCAGCGTGTACTATTAGCGCGAGCATTGTTAAATCGCCCGCAATTATTAGTGCTGGATg                               >  1:575795/1‑139 (MQ=255)

                                                                                                gaTATTTTGCCTGCACTGAAACGTGTCCAGGCCGAGCACCTGATTAACGCACCGATGCAAAAGCTCTCTGGTGGCGAAACGCa                                                                                       >  1:812138/1‑83 (MQ=255)

                                                                                                gaTATTTTGCCTGCACTGAAACGTGTCCAGGCCGAGCACCTGATTAACGCACCGATGCAAAAGCTCTCTGGTGGCGAAACGCa                                                                                       <  2:812138/83‑1 (MQ=255)

                                                                                                gaTATTTTGCCTGCACTGAAACGTGTCCAGGCCGAGCACCTGATTAACGCACCGATGCAAAAGCTCTCTGGTGGCGAAACGCAGCGTGTACTATTAGCGCGAGCATTGTTAAATCGCCCGCAATTATTAGTGCTGGAt                                >  1:868790/1‑138 (MQ=255)

                                                                                                gaTATTTTGCCTGCACTGAAACGTGTCCAGGCCGAGCACCTGATTAACGCACCGATGCAAAAGCTCTCTGGTGGCGAAACGCAGCGTGTACTATTAGCGCGAGCATTGTTAAATCGCCCGCAATTATTAGTGCTGGAt                                <  2:868790/138‑1 (MQ=255)

                                                                                                 atatTTTGCCTGCACTGAAACGTGTCCAGGCCGAGCACCTGATTAACGCACCGAAGCAAGAGCTCTCTGGTGGCGAAACGCAGCGTGTACTATTAGCGCGAGCATTGTTAAATCGCGCGCGATGATTAGTGCTGGATGa                              >  1:905753/1‑139 (MQ=255)

                                                                                                  tatTTTGCCTGCACTGAAACGTGTCCAGGCCGAGCACCTg                                                                                                                                >  1:322755/1‑40 (MQ=255)

                                                                                                  tatTTTGCCTGCACTGAAACGTGTCCAGGCCGAGCACCTg                                                                                                                                <  2:322755/40‑1 (MQ=255)

                                                                                                   atTTTGCCTGCACTGAAACGTGTCCAGGCCGAGCACCTGATTAACGCACCGATGCAAAAGCTCTCTGGTGGCGAAACGCAGCGTGTACTATTAGCGCGAGCATTGTTAAATCGc                                                     <  2:483740/114‑1 (MQ=255)

                                                                                                   atTTTGCCTGCACTGAAACGTGTCCAGGCCGAGCACCTGATTAACGCACCGATGCAAAAGCTCTCTGGTGGCGAAACGCAGCGTGTACTATTAGCGCGAGCATTGTTAAATCGc                                                     >  1:483740/1‑114 (MQ=255)

                                                                                                            gCACTGAAACGTGTCCAGGCCGAGCACCTGATTAACGCACCGATGCAAAAGCTCTCTGGTGGCGAAACGCAGCGTATACTATTAGCGCGAGCATTGTTAAATCGCCCGCAATTATTAGTGc                                     >  1:172478/1‑121 (MQ=255)

                                                                                                            gCACTGAAACGTGTCCAGGCCGAGCACCTGATTAACGCACCGATGCAAAAGCTCTCTGGTGGCGAAACGCAGCGTATACTATTAGCGCGAGCATTGTTAAATCGCCCGCAATTATTAGTGc                                     <  2:172478/121‑1 (MQ=255)

                                                                                                              aCTGAAACGTGTCCAGGCCGAGCACCTGATTAACGCACCGATGCAAAAGCTCTCTGGTGGCGAAACGCAGCGTGTACTATTAGCGCGAGCATTGTTAAATCGCCCGCAATTATTAGTGCTGGATGAACCCACTCAAGGc                 <  2:442681/139‑1 (MQ=255)

                                                                                                                  aaaCGTGTCCAGGCCGAGCACCTGATTAACGCACCGATGCAAAAGCTCTCTGGTGGCGAAACGCa                                                                                       >  2:358091/1‑65 (MQ=255)

                                                                                                                  aaaCGTGTCCAGGCCGAGCACCTGATTAACGCACCGATGCAAAAGCTCTCTGGTGGCGAAACGCa                                                                                       <  1:358091/65‑1 (MQ=255)

                                                                                                                  aaaCGTGTCCAGGCCGAGCACCTGATTAACGCACCGATGCAAAAGCTCTCTGGTGGCGAAACGCAGCGTGTACTATTAGCGCGAGCATTGTTAAATCGCCCGCAATTATTAGGGCTGGATGAACCCACTCAAGGCGTgg             >  2:592412/1‑139 (MQ=255)

                                                                                                                       tgtCCAGGCCGAGCACCTGATTAACGCACCGATGCAAAAGCTCTCTGGTGGCGAAACGCAGCGTGTACTATTAGCGCGAGCATTGTTAAATCGCCCGCAATTATTAGTGCTGGATGAACCCACTCAAGGCGTGGATGTa        >  2:724334/1‑139 (MQ=255)

                                                                                                                         tCCAGGCCGAGCACCTGATTAACGCACCGATGCAAAAGCTCTCTGGTGGCGAAACGCAGCGTGTACTATTAGCGCGAGCATTGTTAAATCGCCCGCAATTATTAGTGCTGGATGAACCCACTCAAGGCGTGGATGTaaa      <  1:731693/139‑1 (MQ=255)

                                                                                                                             ggCCGAGCACCTGATTAACGCACCGATGCAAAAGCTCTCTGGTGGCGAAACGCAGCGTGTACTATTAGCGCGAGCATTGTTAAATCGCCCGCAATTATTAGTGCTGGATGAACCCACTCAAGGCGTGGATGTAAATGGc  <  1:852271/139‑1 (MQ=255)

CGCATCGGCTATGTACCGCAGAAGCTGTATCTCGACACCACGTTGCCACTGACCGTAAACCGTTTTTTACGCTTACGCCCTGGTACACATAAAGAAGATATTTTGCCTGCACTGAAACGTGTCCAGGCCGGGCACCTGATTAACGCACCGATGCAAAAGCTCTCTGGTGGCGAAACGCAGCGTGTACTATTAGCGCGAGCATTGTTAAATCGCCCGCAATTATTAGTGCTGGATGAACCCACTCAAGGCGTGGATGTAAATGGC  >  NC_000913/1942863‑1943126

Alignment Legend
Aligned base mismatch/match (shaded by quality score): `ATCG/ATCG` `< 3 ≤` `ATCG/ATCG` `< 16 ≤` `ATCG/ATCG` `< 34 ≤` `ATCG/ATCG` `< 39 ≤` `ATCG/ATCG` `< 40 ≤` `ATCG/ATCG`
Unaligned base: `atcg` Masked matching base: `atcg` Alignment gap: `‑` Deleted base: `‑`

GATK/CNVnator alignment

N/A