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
A2 F1 I2 R1 78 65.3 3016648 94.6% 2853749 111.9

Breseq alignment

BRESEQ :: Evidence
Predicted mutation
evidence seq id position mutation annotation gene description
RA NC_000913 1,699,194 T→C intergenic (‑14/‑161) malI ← / → malX transcriptional repressor of Mal regulon/maltose and glucose‑specific PTS enzyme IIB component and IIC component

Read alignment evidence...
  seq id position ref new freq score (cons/poly) reads annotation genes product
*NC_0009131,699,1940TC100.0% 213.9 / NA 56intergenic (‑14/‑161)malI/malXtranscriptional repressor of Mal regulon/maltose and glucose‑specific PTS enzyme IIB component and IIC component
Reads supporting (aligned to +/- strand):  ref base T (0/0);  new base C (25/31);  total (25/31)

CGCGTTCTCCTGTGGCGGTAGAGATTCGCCCTTTGCCACTAAGCACCAGCGAAACGGTACTTACCGACACGCCCGCAGCCAGCGCAACATCATGAATGGTTATTTTTTTGGCGGTAGCCATGCAGATGACCTACTCCCTGATTATGTGACAGATAAAACGTTTTACCTTTTATTTATCTTATACCCGCTATTATCGTTGCGTAATGTGATTTATGCCTCACTAAAATTTGATAAAACGTTTTATCTTCTCGCGCAATTTACTG  >  NC_000913/1699060‑1699322
                                                                                                                                      |                                                                                                                                
cgcgTTCTCCTGTGGCGGTAGAGATTCGCCCTTTGCCACTAAGCACCAGCGAAACGGTACTTACCGACACGCCCGCAGCCAGCGCAACATCATGAATGGTTATTTTTTTGGCGGTAGCCATGCAGATGACCTACCCCCt                                                                                                                              <  1:366834/139‑1 (MQ=255)
cgcgTTCTCCTGTGGCGGTAGAGATTCGCCCTTTGCCACTAAGCACCAGCGAAACGGTACTTACCGACACGCCCGCAGCCAGCGCAACATCATGAATGGTTATTTTTTTGGCGGTAGCCATGCAGATGACCTACCCCCt                                                                                                                              <  2:532240/139‑1 (MQ=255)
cgcgTTCTCCTGTGGCGGTAGAGATTCGCCCTTTGCCACTAAGCACCAGCGAAACGGTACTTACCGACACGCCCGCAGCCAGCGCAACATCATGAATGGTTATTTTTTTGGCGGTAGCCATGCAGATGACCTACCCCCt                                                                                                                              <  1:588969/139‑1 (MQ=255)
  cgTTCTCCTGTGGCGGTAGAGATTCGCCCTTTGCCACTAAGCACCAGCGAAACGGTACTTACCGACACGCCCGCAGCCAGCGCAACATCATGAATGGTTATTTTTTTGGCGGTAGCCATGCAGATGACCTACCCCCTGa                                                                                                                            <  2:83209/139‑1 (MQ=255)
             ggCGGTAGAGATTCGCCCTTTGCCACTAAGCACCAGCGAAACGGTACTTACCGACACGCCCGCAGCCAGCGCAACATCATGAATGGTTATTTTTTTGGCGGTAGCCATGCAGATGACCTAcccc                                                                                                                                >  2:795246/1‑124 (MQ=255)
                  tAGAGATTCCCCCTTTGCCACTAAGCACCAGCGAAACGGTACTTACCGACACGCCCGCAGCCAGCGCAACATCATGAATGGTTATTTTTTTGGCGGTAGCCATGCAGATGACCTACCCCCTGATTATGTGACAGATaaa                                                                                                            <  2:1131738/139‑1 (MQ=255)
                      gaTTCGCCCTTTGCCACTAAGCACCAGCGAAACGGTACTTACCGACACGCCCGCAGCCAGCGCAACATCATGAATGGTTATTTTTTTGGCGGTAGCCATGCAGATGACCTACCCCCTGATTATGTGACAGATaa                                                                                                             >  2:106053/1‑134 (MQ=255)
                      gaTTCGCCCTTTGCCACTAAGCACCAGCGAAACGGTACTTACCGACACGCCCGCAGCCAGCGCAACATCATGAATGGTTATTTTTTTGGCGGTAGCCATGCAGATGACCTACCCCCTGATTATGTGACAGATaa                                                                                                             <  1:106053/134‑1 (MQ=255)
                            cccTTTGCCACTAAGCACCAGCGAAACGGTACTTACCGACACGCCCGCAGCCAGCGCAACATCATGAATGGTTATTTTTTTGGCGGTAGCCATGCAGATGACCTACCCCCTGATTATGTGACAGATAAAACGttt                                                                                                      >  2:312461/1‑135 (MQ=255)
                            cccTTTGCCACTAAGCACCAGCGAAACGGTACTTACCGACACGCCCGCAGCCAGCGCAACATCATGAATGGTTATTTTTTTGGCGGTAGCCATGCAGATGACCTACCCCCTGATTATGTGACAGATAAAACGttt                                                                                                      <  1:312461/135‑1 (MQ=255)
                                  gCCACTAAGCACCAGCGAAACGGTACTTACCGACACGCCCGCAGCCAGCGCAACATCATGAATGGTTATTTTTTTGGCGGTAGCCATGCAGATGACCTACCCCCTGATTATGTGACAGATAAAACGTTTTACCTtttat                                                                                            <  1:475516/139‑1 (MQ=255)
                                   ccACTAAGCACCAGCGAAACGGTACTTACCGACACGCCCGCAGCCAGCGCAACATCATGAATGGTTATTTTTTTGGCGGTAGCCATGCAGATGACCTACCCCCTGATTATGTGACAGATAAAACGTTTTACCTtttatt                                                                                           <  1:1495678/139‑1 (MQ=255)
                                            aCCAGCGAAACGGTACTTACCGACACGCCCGCAGCCAGCGCAACATCATGAATGGTTATTTTTTTGGCGGTAGCCATGCAGATGACCTACCCCCTGATTATGTGACAGATAAAACGTTTTACCTTTTATTTATCTtata                                                                                  <  1:456866/139‑1 (MQ=255)
                                              cAGCGAAACGGTACTTACCGACACGCCCGCAGCCAGCGCAACATCATGAATGGTTATTTTTTTGGCGGTAGCCATGCAGATGACCTACCCCCTGATTATGTGACAGATAAAACGTTTTAcc                                                                                                  <  1:505218/121‑1 (MQ=255)
                                              cAGCGAAACGGTACTTACCGACACGCCCGCAGCCAGCGCAACATCATGAATGGTTATTTTTTTGGCGGTAGCCATGCAGATGACCTACCCCCTGATTATGTGACAGATAAAACGTTTTAcc                                                                                                  >  2:505218/1‑121 (MQ=255)
                                               aGCGAAACGGTACTTACCGACACGCCCGCAGCCAGCGCAACATCATGAATGGTTATTTTTTTGGCGGTAGCCATGCAGATGACCTACCCCCTGATTATGTGACAGATAAAACGTTTTACCTTTTATTTATCTTATAccc                                                                               >  2:487500/1‑139 (MQ=255)
                                               aGCGAAACGGTACTTACCGACACGCCCGCAGCCAGCGCAACATCATGAATGGTTATTTTTTTGGCGGTAGCCATGCAGATGACCTACCCCCTGATTATGTGACAGATAAAACGTTTTACCTTTTATTTATCTTATAccc                                                                               <  1:1071882/139‑1 (MQ=255)
                                                 cGAAACGGTACTTACCGACACGCCCGCAGCCAGCGCAACATCATGAATGGTTATTTTTTTGGCGGTAGCCATGCAGATGACCTACCCCCTGATTATGTGACAGATAAAACGttt                                                                                                      <  2:1278472/114‑1 (MQ=255)
                                                 cGAAACGGTACTTACCGACACGCCCGCAGCCAGCGCAACATCATGAATGGTTATTTTTTTGGCGGTAGCCATGCAGATGACCTACCCCCTGATTATGTGACAGATAAAACGttt                                                                                                      >  1:1278472/1‑114 (MQ=255)
                                                   aaaCGGTACTTACCGACACGCCCGCAGCCAGCGCAACATCATGAATGGTTATTTTTTTGGCGGTAGCCATGCAGATGACCTACCCCCTGATTATGTGACAGATAAAACGTTTTAcc                                                                                                  >  2:1348115/1‑116 (MQ=255)
                                                   aaaCGGTACTTACCGACACGCCCGCAGCCAGCGCAACATCATGAATGGTTATTTTTTTGGCGGTAGCCATGCAGATGACCTACCCCCTGATTATGTGACAGATAAAACGTTTTAcc                                                                                                  <  1:1348115/116‑1 (MQ=255)
                                                        gTACTTACCGACACGCCCGCAGCCAGCGCAACATCATGAATGGTTATTTTTTTGGCGGTAGCCATGCAGATGACCTACCCCCTGATTATGTGACAGATAAAACGTTTTACCTTTTATTTATCTTATACCCGCTATTATc                                                                      <  1:413350/139‑1 (MQ=255)
                                                              aCCGACACGCCCGCAGCCAGCGCAACATCATGAATGGTTATTTTTTTGGCGGTAGCCATGCAGATGACCTACCCCCTGATTATGTGACAGATAAAACGTTTTACCTtttat                                                                                            >  2:1487309/1‑111 (MQ=255)
                                                              aCCGACACGCCCGCAGCCAGCGCAACATCATGAATGGTTATTTTTTTGGCGGTAGCCATGCAGATGACCTACCCCCTGATTATGTGACAGATAAAACGTTTTACCTtttat                                                                                            <  1:1487309/111‑1 (MQ=255)
                                                              aCCGACACGCCCGCAGCCAGCGCAACATCATGAATGGTTATTTTTTTGGCGGTAGCCATGCAGATGACCTACCCCCTGATTATGTGACAGATAAAACGTTTTACCTTTTATTTATCTTATACCCGCTATTATCGTTGCg                                                                >  2:1332154/1‑139 (MQ=255)
                                                                   cacGCCCGCAGCCAGCGCAACATCATGAATGGTTATTTTTTTGGCGGTAGCCATGCAGATGACCTACCCCCTGATTATGTGACAGATAAAACGTTTTACCTTTTATTTATCTTATACCCGCTATTATCGTTGCGTAAtg                                                           <  1:813323/139‑1 (MQ=255)
                                                                     cGCCCGCAGCCAGCGCAACATCATGAATGGTTATTTTTTTGGCGGTAGCCATGCAGATGACCTACCCCCTGATTATGTGACAGATAAAACGTTTTACCTtttat                                                                                            >  1:284500/1‑104 (MQ=255)
                                                                     cGCCCGCAGCCAGCGCAACATCATGAATGGTTATTTTTTTGGCGGTAGCCATGCAGATGACCTACCCCCTGATTATGTGACAGATAAAACGTTTTACCTtttat                                                                                            <  2:284500/104‑1 (MQ=255)
                                                                      gCCCGCAGCCAGCGCAACATCATGAATGGTTATTTTTTTGGCGGTAGCCATGCAGATGACCTACCCCCTGATTATGTGACAGATAAAACGTTTTACCTTTTATTTATCTTATACCCGCTATTATCGTTGCGTAAtg                                                           <  1:409913/136‑1 (MQ=255)
                                                                      gCCCGCAGCCAGCGCAACATCATGAATGGTTATTTTTTTGGCGGTAGCCATGCAGATGACCTACCCCCTGATTATGTGACAGATAAAACGTTTTACCTTTTATTTATCTTATACCCGCTATTATCGTTGCGTAAtg                                                           >  2:409913/1‑136 (MQ=255)
                                                                      gCCCGCAGCCAGCGCAACATCATGAATGGTTATTTTTTTGGCGGTAGCCATGCAGATGACCTACCCCCTGATTATGTGACAGATAAAACGTTTTACCTTTTATTTATCTTATACCCGCTATTATCGTTGCGTAATGTGa                                                        >  2:784465/1‑139 (MQ=255)
                                                                           cagccagcGCAACATCATGAATGGTTATTTTTTTGGCGGTAGCCATGCAGATGACCTACCCCCTGATTATGTGACAGATAAAACGTTTTACCTTTTATTTATCTTATACCCGCTATTATCGTTGCGTAATGTGATTTAt                                                   >  2:338149/1‑139 (MQ=255)
                                                                                agcGCAACATCATGAATGGTTATTTTTTTGGCGGTAGCCATGCAGATGACCTACCCCCTGATTATGTGACAGATAAAACGTTTTACCTTTTATTTATCTtat                                                                                   >  2:710085/1‑102 (MQ=255)
                                                                                agcGCAACATCATGAATGGTTATTTTTTTGGCGGTAGCCATGCAGATGACCTACCCCCTGATTATGTGACAGATAAAACGTTTTACCTTTTATTTATCTtat                                                                                   <  1:710085/102‑1 (MQ=255)
                                                                                  cgcAACATCATGAATGGTTATTTTTTTGGCGGTAGCCATGCAGATGACCTACCCCCTGATTATGTGACAGATAAAACGTTTTACCTTTTATTTATCTTATACCCGCtat                                                                          <  2:15756/109‑1 (MQ=255)
                                                                                  cgcAACATCATGAATGGTTATTTTTTTGGCGGTAGCCATGCAGATGACCTACCCCCTGATTATGTGACAGATAAAACGTTTTACCTTTTATTTATCTTATACCCGCtat                                                                          >  1:15756/1‑109 (MQ=255)
                                                                                  cgcAACATCATGAATGGTTATTTTTTTGGCGGTAGCCATGCAGATGACCTACCCCCTGATTATGTGACAGATAAAACGTTTTACCTTTTATTTATCTTATACCCGCTATTATc                                                                      <  1:1159878/113‑1 (MQ=255)
                                                                                  cgcAACATCATGAATGGTTATTTTTTTGGCGGTAGCCATGCAGATGACCTACCCCCTGATTATGTGACAGATAAAACGTTTTACCTTTTATTTATCTTATACCCGCTATTATc                                                                      >  2:1159878/1‑113 (MQ=255)
                                                                                  cgcAACATCATGAATGGTTATTTTTTTGGCGGTAGCCATGCAGATGACCTACCCCCTGATTATGTGACAGATAAAACGTTTTACCTTTTATTTATCTTATACCCGCTATTATCGTTGCGTAATGTGATTTATGCCTCAc                                            >  1:672796/1‑139 (MQ=255)
                                                                                         tcatGAATGGTTATTTTTTTGGCGGTAGCCATGCAGATGACCTACCCCCTGATTATGTGACAGATAAAACGTTTTACCTTTTATTTATCTTATACCCGCTATTATCGTTGCGTAATGTGATTTATGCCTCACTAAAAtt                                     <  1:1332154/139‑1 (MQ=255)
                                                                                            tGAATGGTTATTTTTTTGGCGGTAGCCATGCAGATGACCTACCCCCTGATTATGTGACAGATAAAACGTTTTACCTtttat                                                                                            >  1:845734/1‑81 (MQ=255)
                                                                                            tGAATGGTTATTTTTTTGGCGGTAGCCATGCAGATGACCTACCCCCTGATTATGTGACAGATAAAACGTTTTACCTtttat                                                                                            <  2:845734/81‑1 (MQ=255)
                                                                                            tGAATGGTTATTTTTTTGGCGGTAGCCATGCAGATGACCTACCCCCTGATTATGTGACAGATAAAACGTTTTACCTTTTATTTATCTTATACCCGCTATTATCGTTGCGTAAt                                                            >  2:1130598/1‑113 (MQ=255)
                                                                                            tGAATGGTTATTTTTTTGGCGGTAGCCATGCAGATGACCTACCCCCTGATTATGTGACAGATAAAACGTTTTACCTTTTATTTATCTTATACCCGCTATTATCGTTGCGTAAt                                                            <  1:1130598/113‑1 (MQ=255)
                                                                                                 ggTTATTTTTTTGGCGGTAGCCATGCAGATGACCTACCCCCTGATTATGTGACAGATAAAACGTTTTACCtt                                                                                                >  2:1273111/1‑72 (MQ=255)
                                                                                                 ggTTATTTTTTTGGCGGTAGCCATGCAGATGACCTACCCCCTGATTATGTGACAGATAAAACGTTTTACCtt                                                                                                <  1:1273111/72‑1 (MQ=255)
                                                                                                  gTTATTTTTTTGGCGGTAGCCATGCAGATGACCTACCCCCTGATTATGTGACAGATAAAACGTTTTACCTTTTATTTATCTTATACCCGCTATTATCGTTGCGTAATGTGATTTATGCCTCACTAAAATTTGATAAAAc                            >  1:967055/1‑139 (MQ=255)
                                                                                                   ttATTTTTTTGGCGGTAGCCATGCAGATGACCTACCCCCTGATTATGTGACAGATAAAACGTTTTACCTTTTATTTATCTTATACCCGCTATTATCGTTGCGTAATGTGATTTATGCCTCACTAAAATTTGATAAAACg                           >  2:868588/1‑139 (MQ=255)
                                                                                                     aTTTTTTTGGCGGTAGCCATGCAGATGACCTACCCCCt                                                                                                                              <  2:240412/38‑1 (MQ=255)
                                                                                                     aTTTTTTTGGCGGTAGCCATGCAGATGACCTACCCCCt                                                                                                                              >  1:240412/1‑38 (MQ=255)
                                                                                                      tttttttGGCGGTAGCCATGCAGATGACCTACCCCCTGATTATGTGACAGATAAAACGTTTTACCTTTTATTTATCTTATAcc                                                                                <  2:758237/83‑1 (MQ=255)
                                                                                                      tttttttGGCGGTAGCCATGCAGATGACCTACCCCCTGATTATGTGACAGATAAAACGTTTTACCTTTTATTTATCTTATAcc                                                                                >  1:758237/1‑83 (MQ=255)
                                                                                                             ggCGGTAGCCATGCAGATGACCTACCCCCTGATTATGTGACAGATAAAACGTTTTACCTTTTATTTATCTTATAccc                                                                               >  2:518836/1‑77 (MQ=255)
                                                                                                             ggCGGTAGCCATGCAGATGACCTACCCCCTGATTATGTGACAGATAAAACGTTTTACCTTTTATTTATCTTATAccc                                                                               <  1:518836/77‑1 (MQ=255)
                                                                                                                 gTAGTCATGCAGATTACCTACCCCCTGATTATGTGACAGATAAAACGTTTTACCTTTTATTTATCTTATACCCGCTATTATCGTTGCGTAATGTGATTTATGCCTCACTAAAATTTGATAAAACGTTTTATCTTCTcgc             <  2:967055/139‑1 (MQ=255)
                                                                                                                 gTAGCCATGCAGATGACCTACCCCCTGATTATGTGACAGATAAAACGTTTTACCTTTTATTTATCTTATACCCGCTATTATCGTTGCGTAATGTGATTTATGCCTCACTAAAATTTGATAAAACGTTTTATCTTCTcgc             <  1:338149/139‑1 (MQ=255)
                                                                                                                            gATGACCTACCCCCTGATTATGTGACAGATAAAACGTTTTACCTTTTATTTATCTTATACCCGCTATTATCGTTGCGTAATGTGATTTATGCCTCACTAAAATTTGATAAAACGTTTTATCTTCTCGCGCAATTTACTg  >  2:472407/1‑139 (MQ=255)
                                                                                                                                      |                                                                                                                                
CGCGTTCTCCTGTGGCGGTAGAGATTCGCCCTTTGCCACTAAGCACCAGCGAAACGGTACTTACCGACACGCCCGCAGCCAGCGCAACATCATGAATGGTTATTTTTTTGGCGGTAGCCATGCAGATGACCTACTCCCTGATTATGTGACAGATAAAACGTTTTACCTTTTATTTATCTTATACCCGCTATTATCGTTGCGTAATGTGATTTATGCCTCACTAAAATTTGATAAAACGTTTTATCTTCTCGCGCAATTTACTG  >  NC_000913/1699060‑1699322

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