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 F110 I0 R1	32	23.2	500348	95.1%	475830	140.9

Breseq alignment

BRESEQ :: Evidence

Predicted mutation
evidence	seq id	position	mutation	freq	annotation	gene	description
RA	CP000730	2,361,729	G→A	50.3%	P193S (CCA→TCA)	secY1 ←	Sec family Type I general secretory pathway preprotein translocase SecY

Read alignment evidence...
	seq id	position		ref	new	freq	score (cons/poly)	reads	annotation	genes	product
*	CP000730	2,361,729	0	G	A	50.3%	‑1.9 / 35.7	30	P193S (CCA→TCA)	secY1	Sec family Type I general secretory pathway preprotein translocase SecY
Reads supporting (aligned to +/- strand): ref base G (6/9); new base A (9/6); total (15/15)
Fisher's exact test for biased strand distribution p-value = 4.66e-01
Kolmogorov-Smirnov test that lower quality scores support variant p-value = 9.36e-01

ACGAACGGCTTCAAGTACATAAATAGCACCTACAGTTAATAGTATCAGTGACACTAAAAGTCCTAATACTTTCAACCATGCTAATGATGTATCTTCTTGCCCAACGAACGCAGTTTGTCCAAATTGAATTAGACTGGCTGGCAACGTTGATAAAATACCCGCAAATATGATAATAGAAATACCATTACCAACACCGAACTGAGTGATTTGATCACCAAGCCATATTAAGAAAGCAGTTCCTGCTGTCAAAACTAGTGCTATTAATAAATAACTCAT  >  CP000730/2361589‑2361864

cccaaCGCCTTCTAGAAGATTAATAGTACCTACAGTTAATAGTATCAGTGACACTAAAAGTCCTAATACTTTCAACCATGCTAATGATGTATCTTCTTGCCCAACGAACTCAGTGTGCCCAAATTGAATTAGActggctgg                                                                                                                                         <  1:172541/138‑1 (MQ=255)

          taaaGTACATAAATAGCACCTACCGGTAATAGTATCAGTGACACTAAAAGTCCTAATACTTTCAACCATGCTAATGATGTATCTTCTTGCCCAACGAACGCAGTTTGTCCAAATTGAATTAGACTGGCTGACAACGTTGAt                                                                                                                               <  2:19309/139‑1 (MQ=255)

                     aaTAGCACCTACAGTTAATAGTATCAGTGACACTAAAAGTCCTAATACTTTCAACCATGCTAATGATGTATCTTCTTGCCCAACGAACGCAGTTTGTCCAAATTGAATTAGACTGGCTGGCAACGTTGATAAAATACCCGc                                                                                                                    >  1:156945/1‑141 (MQ=255)

                     aaTAGCACCTACAGTTAATAGTATCAGTGACACTAAAAGTCCTAATACTTTCAACCATGCTAATGATGTATCTTCTTGCCCAACGAACGCAGTTTGTCCAAATTGAATTAGACTGGCTGACAACGTTGATAAAATACCCGc                                                                                                                    >  2:36378/1‑141 (MQ=255)

                         gCACCTAACGTTAATAGTATCAGTGACACTAAAAGTCCTAATACTTTCAACCATGCTAATGATGTATCTTCTTGCCCAACGAACGCAGTTTGTCCAAATTGAATTAGACTGGCTGGCAACGTTGATAAAATACCCGCAAat                                                                                                                <  1:201402/141‑1 (MQ=255)

                              tACAGTTAATAGTATCAGTGACACTAAAAGACCTAATACTTTCAACCATGCTAATGAGGTGTCTTCTTGCCCAAAGAAAGCAGATTGTCCAAATTGAATTAGACTGGCTGACAACGATGATAAAATACCCGCAAATAAGaa                                                                                                           >  2:86876/1‑140 (MQ=255)

                                  gTTAATAGTATCAGTGACACTAAAAGTCCTAATACTTTCAACCATGCTAATGATGTATCTTCTTGCCCAACGAACGCAGTTTGTCCAAATTGAATTAGACTGGCTGACAACGTTGATAAAATCCCCGCAAATATGatcata                                                                                                       >  1:155369/1‑141 (MQ=255)

                                   ttAATAGTATCAGTGACACTAAAAGTCCTAATACTTTCAACCATGCTAATGATGTATCTTCTTGCCCAACGAACGCAGTTTGTCCAAATTGAATTAGACTGGCTGGCAACGTTGATAAAATACCCGCAAATATGATAATAg                                                                                                      >  2:139122/1‑141 (MQ=255)

                                    tAATAGTATCAGTGACACTAAAAGTCCTAATACTTTCAACCATGCTAATGATGTATCTTCTTGCCCAACGAACGCAGTTTGTCCAAATTGAATTAGACTGGCTGACAACGTTGATAAAATACCCGCAAATATGataa                                                                                                         >  1:23197/1‑137 (MQ=255)

                                    tAATAGTATCAGTGACACTAAAAGTCCTAATACTTTCAACCATGCTAATGATGTATCTTCTTGCCCAACGAACGCAGTTTGTCCAAATTGAATTAGACTGGCTGACAACGTTGATAAAATACCCGCAAATATGataa                                                                                                         <  2:23197/137‑1 (MQ=255)

                                     aaTAGTATCAGGGACACTAAAAGTCCTAATACTTTCAACCATGCTAATGATGTATCTTCTTGCCCAACGAACGCAGTTTGTCCAAATTGAATTAGACTGGCTGGCAACGTTGATAAAATACCCGCAAATATGATAATAGaa                                                                                                    <  1:96123/141‑1 (MQ=255)

                                      aTAGTATCAGTGACACTAAAAGTCCTAATACTTTCAACCATGCTAATGATGTATCTTCTTGCCCAACGAACGCAGTTTGTCCAAATTGAATTAGACTGGCTGGCAACGTTGATAAAATACCCGCAAATATGATAATAGaaa                                                                                                   <  2:83136/141‑1 (MQ=255)

                                                tGACACTAAAAGTCCTAATACTTTCAACCATGCTAATGATGTATCTTCTTGCCCAACGAACGCAGTTTGTCCAAATTGAATTAGACTGGCTGGCAACGTTGATAAAATACCCGCAAATATGATAATAGAAATACCATTAcc                                                                                         <  1:153542/141‑1 (MQ=255)

                                                             ccTAATACTTTCAACCATGCTAATGATGTATCTTCTTGCCCAACGAACGCAGTGTGGCCAAATTGAATTAGACTGGCTGACAACGTTGATAAAATACCCGCAAATATGATAATAGAAATACCATTACCAACACCGAACTGa                                                                            <  1:47064/141‑1 (MQ=255)

                                                                      ttCAACCATGCTAATGATGTATCTTCTTGCCCAACGAACGCAGTTTGTCCAAATTGAATTAGACTGGCTGGCAACGTTGATAAAATACCCGCAAATATGATATTAGAAATACCATTACCAACACCGTACTGAGTGATTTGa                                                                   <  1:139122/141‑1 (MQ=255)

                                                                      ttCAACCATGCTAATGATGTATCTTCTTGCCCAACGAACGCAGTTTGTCCAAATTGAATTAGACTGGCTGGCAACGTTGATAAAATACCCGCAAATATGATAATAGAAATACCATTACCAACACCGAACTGAGTGATTTGa                                                                   >  1:26781/1‑141 (MQ=255)

                                                                      ttCAACCATGCTAATGATGTATCTTCTTGCCCAACGAACGCAGTTTGTCCAAATTGAATTAGACTGGCTGGCAACGTTGATAAAATACCCACAAATATGATAATAGATGAAAAAGGACGCAAACCGAACTGAGTGATTTGa                                                                   >  2:226444/1‑141 (MQ=255)

                                                                         aaCCATGCTAATGATGTATCTTCTTGCCCAACGAACGCAGTTTGTCCAAATTGAATTAGACTGGCTGACAACGTTGATAAAATACCCGCAAATATGATAATAGAAATACCATTACCAACACCGAACTGAGTGATTTGATcc                                                                >  2:189095/1‑140 (MQ=255)

                                                                          aCCATGCTAATGATGTATCTTCTTGCCCAACGAACGCAGTTTGTCCAAATTGAATTAGACTGGCTGACAACGTTGATAAAATACCCGCAAATATGATAATAGAAATACCATTACCAACACCGAACTGAGTGATTTGATCAc                                                               >  2:71396/1‑141 (MQ=255)

                                                                            cATGCTAATGATGTATCTTCTTGCCCAACGAACGCAGTTTGTCCAAATTGAATTAGACTGGCTGGCAACGTTGATAAAATACCCGCAAATATGATAATAGAAATACCATTACCAACACCGAACTGAGTGATTTGATCACCa                                                             >  2:155212/1‑141 (MQ=255)

                                                                             aTGCTAATGATGTATCTTCTTGCCCAACGAACGCAGTTTGTCCAAATTGAATTAGACTGGCTGACAACGTTGATAAAATACCCGCAAATATGATAATAGAAATACCATTACCAACACCGAACTGAGTGATTTGATCACCaa                                                            >  1:226333/1‑141 (MQ=255)

                                                                             aTGCTAATGATGTATCTTCTTGCCCAACGAACGCAGTTTGTCCAAATTGAATTAGACTGGCTGACAACGTTGATAAAATACCCGCAAATATGATAATAGAAATACCATTACCAACACCGAACTGAGTGATTTGATCACCaa                                                            >  1:226340/1‑141 (MQ=255)

                                                                              tGCTAATGATGTATCGTCTTGCCCAACGAACGCAGTTTGTCCAAATTGAATTAGACTGGCTGACAACGTTGATAAAATACCCGCAAATATGATAATAGAAATACCATTACCAACACCGAACTGAGTGATTTGATCACCAAg                                                           >  1:185570/1‑141 (MQ=255)

                                                                                           tcttctTGCCCAACGAACGCAGTTTGTCCAAATTGAATTAGACTGGCTGGCAACGTTGATAAAATACCCGCAAATATGATAATAGAAATACCATTACCAACACCGAACTGAGTGATTTGATCACCAAGCCATCTTAAGaaa                                              >  1:136602/1‑141 (MQ=255)

                                                                                              tcttGCCCAACGAACGCAGTTTGTCCAAATTGAATTAGACTGGCTGGCAACGTTGATAAAATACCCGCAAATATGATAATAGAAATACCATTACCAACACCGAACTGAGTGATTTGATCACCAAGCCATATTAAGAAAGCa                                           <  1:212187/141‑1 (MQ=255)

                                                                                                  gCCCAACGAACGCCGTTTGTCCAAATTGAATTAGACTGGCTGGCAACGTTGATAAAATACCCGCAAATATGATAATAGAAATCCCATTACCAACACCGAACTGAGTGATTTGATCACCAAGCCATATTAAGAAAGCAGTTc                                       <  2:129983/141‑1 (MQ=255)

                                                                                                     cAACGAACGCAGTTTGGCCAAATTGAATTAGACTGGCTGGCAACGTTGATAAAATATCCGCAAATATGATAATAGAAATACCATTACCAACACCGAACTGAGTGATTTGATCACCAAGCCATATTAAGAAAGCAGTTCctg                                    <  2:145665/141‑1 (MQ=255)

                                                                                                             gCAGTTTGTCCAAATTGCATTAGTCTTGCTGACAACGTTGATAAAATACCCTCAAATATGATAATAGAAATACCATTACCAACACCGAACTGAGTGATTTGATCACCAAGCCATATTAAGAAAGCAGTTCCTGCTGTCaaa                            <  2:170273/141‑1 (MQ=255)

                                                                                                                         aaTTGAATTAGACTGGCTGACAACGTTGATAAAATACCCGCAAATATGATAATAGAAATACCATTACCAACACCGAACTGAGTGATTTGATCACCAAGCCATATTAAGAAAGCAGTTCCTGCTGTCAAAACTAGTGCTAtt                <  2:185570/141‑1 (MQ=255)

                                                                                                                         aaTTGAATTAGACTGGCTGACAACGTTGATAAAATACCCGCAAATATGATAATAGAAATACCATTACCAACACCGAACTGAGTGATTTGATCACCAAGCCATATTAAGAAAGCAGTTCCTGCTGTCAAAACTAGTGCTAtt                <  1:103834/141‑1 (MQ=255)

                                                                                                                                    aCTGGCTCGCAACGTTGATAAAATACCCGCAAATATGATAATAGAAATACAATTACCAACACCGAACTGAGTGATTTGATCACCAAGCCATATTAAGAAAGCAGTTCCTGCTGTCAAAACTAGTGCTATTAATAAATAACt     <  2:2976/141‑1 (MQ=255)

                                                                                                                                       ggctggcCACGTTGATAAAATACCCGCAAATATGATAATAGAAATACCATTACCAACACCGAACTGAGTGATTTGATCACCAAACCATATTAAGAAAGCAGTTCCTGCTGTCAAAACTAGTACTATTAATAAATAACTCAt  >  2:246904/1‑141 (MQ=255)

ACGAACGGCTTCAAGTACATAAATAGCACCTACAGTTAATAGTATCAGTGACACTAAAAGTCCTAATACTTTCAACCATGCTAATGATGTATCTTCTTGCCCAACGAACGCAGTTTGTCCAAATTGAATTAGACTGGCTGGCAACGTTGATAAAATACCCGCAAATATGATAATAGAAATACCATTACCAACACCGAACTGAGTGATTTGATCACCAAGCCATATTAAGAAAGCAGTTCCTGCTGTCAAAACTAGTGCTATTAATAAATAACTCAT  >  CP000730/2361589‑2361864

Alignment Legend
Aligned base mismatch/match (shaded by quality score): `ATCG/ATCG` `< 3 ≤` `ATCG/ATCG` `< 12 ≤` `ATCG/ATCG` `< 22 ≤` `ATCG/ATCG` `< 32 ≤` `ATCG/ATCG` `< 41 ≤` `ATCG/ATCG`
Unaligned base: `atcg` Masked matching base: `atcg` Alignment gap: `‑` Deleted base: `‑`

GATK/CNVnator alignment

N/A