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 I2 R1 780 68.3 3343050 93.5% 3125751 102.9

Breseq alignment

BRESEQ :: Evidence
Predicted mutation
evidence seq id position mutation annotation gene description
RA NC_000913 4,614,260 G→A *260* (TAG→TAA)  yjjV → putative DNase

Read alignment evidence...
  seq id position ref new freq score (cons/poly) reads annotation genes product
*NC_0009134,614,2600GA100.0% 133.0 / NA 42*260* (TAG→TAA) yjjVputative DNase
Reads supporting (aligned to +/- strand):  ref base G (0/0);  new base A (22/20);  total (22/20)

CGGAGCAGGCTGCCCGTGTGTTCGCCGTGCTTTGCGAGTTGCGCCGGGAACCGGCGGATGAGATTGCGCAAGCGTTGCTTAATAACACGTATACGTTGTTTAACGTGCCGTAGGCCGGATAAGGCGTTCACGCCGCATCCGGCAGTTGGCGCACAATGCCTGATGCGACGCTTAACGCGTCTTATCATGCCTACAGGTTTGTGCCGAACCGTAGGCCGGATAAGGCGTTCACGCCGCATCCGGCAGT  >  NC_000913/4614148‑4614394
                                                                                                                |                                                                                                                                      
cGGAGCAGGCTGCCCGTGTGTTCGCCGTGCTTTGCGAGTTGCGCCGGGAACCGGCGGATGAGATTGCGCAAGCGTTGCTTAATAACACGTATACGTTGTTTAACGTGCCGTAAGCCGGATAAGGCGTTCACGCCGCATc                                                                                                              >  2:978376/1‑139 (MQ=255)
            cccGTGTGTTCGCCGTGCTTTGCGAGTTGCGCCGGGAACCGGCGGATGAGATTGCGCAAGCGTTGCTTAATAACACGTATACGTTGTTTAACGTGCCGTAAGCCGGATAAGGCGTTCACGCCGCATCCGGCAGTTGgcg                                                                                                  <  1:978376/139‑1 (MQ=255)
             ccGTGTGTTCGCCGTGCTTTGCGAGTTGCGCCGGGAACCGGCGGATGAGATTGCGCAAGCGTTGCTTAATAACACGTATACGTTGTTTAACGTGCCGTAAGCCGGATAAGGCGTTCACGCCGCATCCGGCAGTTGgcgc                                                                                                 >  1:264217/1‑139 (MQ=255)
                         cGTGCTTTGCGAGTTGCGCCGGGAACCGGCGGATGAGATTGCGCAAGCGTTGCTTAATAACACGTATACGTTGTATAACGTGCCGTAAGCCGGATAATGCGTTCACGCCGCATCCGGCAGTTGGCGCACAATGCCTGAt                                                                                     >  2:135595/1‑139 (MQ=255)
                                tGCGAGTTGCGCCGGGAACCGGCGGATGAGATTGCGCAAGCGTTGCTTAATAACACGTATACGTTGTTTAACGTGCCGTAAGCCGGATAAGGCGTTCACGCCGCATCCGGCAGTTGGCACACAATGCCTGATGCGACGc                                                                              >  1:473191/1‑139 (MQ=255)
                                    aGTTGCGCCGGGAACCGGCGGATGAGATTGCGCAAGCGTTGCTTAATAACACGTATACGTTGTTTAACGTGCCGTAAGCCGGATAAGGCGTTCACGCCGCATCCGGCAGTTGGCGCACAATGCCTGATGCGACGCTTaa                                                                          <  1:135595/139‑1 (MQ=255)
                                     gTTGCGCCGGGAACCGGCGGATGAGATTGCGCAAGCGTTGCTTAATAACACGTATACGTTGTTTAACGTGCCGTAAGCCGGATAAGGCGTTCACGCCGCATCCGGCAGTTGGCGCACAATGCCTGATGCGACGCTTAAc                                                                         >  2:11963/1‑139 (MQ=255)
                                        gcgcCGGGAACCGGCGGATGAGATTGCGCAAGCGTTGCTTAATAACACGTATACGTTGTTTAACGTGCCGTAAGCCGGATAAGGCGTTCACGCCGCATCCGGCAGTTGGCGCACAATGCCTGATGCGACg                                                                               >  1:1437982/1‑130 (MQ=255)
                                        gcgcCGGGAACCGGCGGATGAGATTGCGCAAGCGTTGCTTAATAACACGTATACGTTGTTTAACGTGCCGTAAGCCGGATAAGGCGTTCACGCCGCATCCGGCAGTTGGCGCACAATGCCTGATGCGACg                                                                               <  2:1437982/130‑1 (MQ=255)
                                                                tGCGCAAGCGTTGCTTAATAACACGTATACGTTGTTTAACGTGCCGTAAGCCGGATAAGGCg                                                                                                                           >  2:97716/1‑62 (MQ=255)
                                                                tGCGCAAGCGTTGCTTAATAACACGTATACGTTGTTTAACGTGCCGTAAGCCGGATAAGGCg                                                                                                                           <  1:97716/62‑1 (MQ=255)
                                                                       gCGTTGCTTAATAACACGTATACGTTGTTTAACGTGCCGTAAGCCGGATAAGGCGTTCACGCCGCATCCGGCAGTTGGCGCACAATGCCTGATGCGACGCTTAACGCGTCTTAt                                                                <  2:650529/114‑1 (MQ=255)
                                                                       gCGTTGCTTAATAACACGTATACGTTGTTTAACGTGCCGTAAGCCGGATAAGGCGTTCACGCCGCATCCGGCAGTTGGCGCACAATGCCTGATGCGACGCTTAACGCGTCTTAt                                                                >  1:650529/1‑114 (MQ=255)
                                                                       gCGTTGCTTAATAACACGTATACGTTGTTTAACGTGCCGTAAGCCGGATAAGGCGTTCACGCCGCATCCGGCAGTTGGCGCACAATGCCTGATGCGACGCTTAACGCGTCTTATCGTGCCTa                                                        <  1:298775/122‑1 (MQ=255)
                                                                       gCGTTGCTTAATAACACGTATACGTTGTTTAACGTGCCGTAAGCCGGATAAGGCGTTCACGCCGCATCCGGCAGTTGGCGCACAATGCCTGATGCGACGCTTAACGCGTCTTATCGTGCCTa                                                        >  2:298775/1‑122 (MQ=255)
                                                                        cGTTGCTTAATAACACGTATACGTTGTTTAACGTGCCGTAAGCCGGATAAGGCGTTCACGCCGCATCCGGc                                                                                                          >  1:1231099/1‑71 (MQ=255)
                                                                        cGTTGCTTAATAACACGTATACGTTGTTTAACGTGCCGTAAGCCGGATAAGGCGTTCACGCCGCATCCGGc                                                                                                          <  2:1231099/71‑1 (MQ=255)
                                                                           tGCTTAATAACACGTATACGTTGTTTAACGTGCCGTAAGCCGGATAAGGCGTTCACGCCGCATCCGGCAGTTGGCGCACAATGCCTGATGCGACGCTTAACGCGTCTTATCATGCCTACAGGTTTGTGCCGAACCGTAg                                   <  1:11963/139‑1 (MQ=255)
                                                                            gCTTAATAACACGTATACGTTGTTTAACGTGCCGTAAGCCGGATAAGGCGTTCAcg                                                                                                                     <  1:631133/56‑1 (MQ=255)
                                                                            gCTTAATAACACGTATACGTTGTTTAACGTGCCGTAAGCCGGATAAGGCGTTCAcg                                                                                                                     >  2:631133/1‑56 (MQ=255)
                                                                            gCTTAATAACACGTATACGTTGTTTAACGTGCCGTAAGCCGGATAAGGCGTTCACGCCGCATCCGGCAGTTGGCGCACAATGCCTGATGCGACGCTTAACGCGTCTTATc                                                               <  1:1415328/110‑1 (MQ=255)
                                                                            gCTTAATAACACGTATACGTTGTTTAACGTGCCGTAAGCCGGATAAGGCGTTCACGCCGCATCCGGCAGTTGGCGCACAATGCCTGATGCGACGCTTAACGCGTCTTATc                                                               >  2:1415328/1‑110 (MQ=255)
                                                                            gCTTAATAACACGTATACGTTGTTTAACGTGCCGTAAGCCGGATAAGGCGTTCACGCCGCATCCGGCAGTTGGCGCACAATGCCTGATGCGACGCTTAACGCGTCTTATc                                                               >  2:1162756/1‑110 (MQ=255)
                                                                            gCTTAATAACACGTATACGTTGTTTAACGTGCCGTAAGCCGGATAAGGCGTTCACGCCGCATCCGGCAGTTGGCGCACAATGCCTGATGCGACGCTTAACGCGTCTTATc                                                               <  1:1162756/110‑1 (MQ=255)
                                                                             cTTAATAACACGTATACGTTGTTTAACGTGCCGTAAGCCGGATAAGGCGTTCACGCCGCATCCGGCAGTTGGCACACAATGCCTGATGCGACGCTTAACGCGTCTTATCATGCCTACAGGTTTGTGCCGAACCGTAGGc                                 <  2:473191/139‑1 (MQ=255)
                                                                                       cGTATACGTTGTTTAACGTGCCGTAAGCCGGATAAGGCGTTCACGCCGCATCCgtc                                                                                                          <  1:1002727/56‑3 (MQ=25)
                                                                                       cGTATACGTTGTTTAACGTGCCGTAAGCCGGATAAGGCGTTCACGCCGCATCCGGc                                                                                                          >  2:1002727/1‑56 (MQ=255)
                                                                                          ataCGTTGTTTAACGTGCCGTAAGCCGGATAAGGCGTTCACGCCGCATCCGGc                                                                                                          >  2:1001358/1‑53 (MQ=255)
                                                                                          ataCGTTGTTTAACGTGCCGTAAGCCGGATAAGGCGTTCACGCCGCATCCGGc                                                                                                          <  1:1001358/53‑1 (MQ=255)
                                                                                          ataCGTTGTTTAACGTGCCGTAAGCCGGATAAGGCGTTCACGCCGCATCCGGCAGTTGGCGCACAATGCCTGATGCg                                                                                  <  1:488953/77‑1 (MQ=255)
                                                                                          ataCGTTGTTTAACGTGCCGTAAGCCGGATAAGGCGTTCACGCCGCATCCGGCAGTTGGCGCACAATGCCTGATGCg                                                                                  >  2:488953/1‑77 (MQ=255)
                                                                                          ataCGTTGTTTAACGTGCCGTAAGCCGGATAAGGCGTTCACGCCGCATCCGGCAGTTGGCGCACAATGCCTGATGCGACGCTTAACGCGTCTTATCATGCCTACAGGTTTGTGCCGAACCGTAGGCCGGATAAGGCGtt                    <  2:264217/139‑1 (MQ=255)
                                                                                                tgttTAACGTGCCGTAAGCCGGATAAGGCGTTCACGCCGCATCCGGCAGTTGGCGCACAATGCCTGATGCGACGCTTAACGCGTCTTATCATGCCTACAGGTTTGTGCCGAAcc                                       >  2:1503176/1‑114 (MQ=255)
                                                                                                tgttTAACGTGCCGTAAGCCGGATAAGGCGTTCACGCCGCATCCGGCAGTTGGCGCACAATGCCTGATGCGACGCTTAACGCGTCTTATCATGCCTACAGGTTTGTGCCGAAcc                                       <  1:1503176/114‑1 (MQ=255)
                                                                                                  tttAACGTGCCGTAAGCCGGATAAGGCGTTCACGCCGCATCCGGCAGTTGGCGCACAATGCCTGATGCGACGCTTAACGCGTCTTATCATGCCTACAGGTTTGTGCCGAACCGTAGGCCGGATAAGGCGTTCAcgccgc            >  2:1427099/1‑139 (MQ=255)
                                                                                                  tttAACGTGCCGTAAGCCGGATAAGGCGTTCACGCCGCATCCGGCAGTTGGCGCACAATGCCTGATGCGACGCTTAACGCGTCTTATCATGCCTACAGGTTTGTGCCGAACCGTAGGCCGGATAAGGCGTTCAcgccgc            >  1:1060471/1‑139 (MQ=255)
                                                                                                          gCCGTAAGCCGGATAAGGCGTTCACGCCGCATCCGGc                                                                                                          >  1:545157/1‑37 (MQ=255)
                                                                                                          gCCGTAAGCCGGATAAGGCGTTCACGCCGCATCCGGc                                                                                                          <  2:545157/37‑1 (MQ=11)
                                                                                                          gCCGTAAGCCGGATAAGGCGTTCACGCCGCATCCGGCAGtt                                                                                                      <  2:1328215/41‑1 (MQ=255)
                                                                                                          gCCGTAAGCCGGATAAGGCGTTCACGCCGCATCCGGCAGtt                                                                                                      >  1:1328215/1‑41 (MQ=255)
                                                                                                           ccGTAAGCCGGATAAGGCGTTCACGCCGCATCCGGCAGTTGGCGCACAATGCCTGATGCGACGCTTAACGCGTCTTATCATGCCTACAGGTTTGTGCCGAACCGTAGGCCGGATAAGGCGTTCACGCCGCATCCGGCAg   <  2:919678/139‑1 (MQ=255)
                                                                                                            cGTAAGCCGGATAAGGCGTTCACGCCGCATCCGGCAGTTGGCGCACAATGCCTGATGCGACGCTTAACGCGTCTTATCATGCCTACAGGTTTGTGCCGAACCGTAGGCCGGATAAGGCGTTCACGCCGCATCCGGCAGt  >  1:207142/1‑139 (MQ=255)
                                                                                                                |                                                                                                                                      
CGGAGCAGGCTGCCCGTGTGTTCGCCGTGCTTTGCGAGTTGCGCCGGGAACCGGCGGATGAGATTGCGCAAGCGTTGCTTAATAACACGTATACGTTGTTTAACGTGCCGTAGGCCGGATAAGGCGTTCACGCCGCATCCGGCAGTTGGCGCACAATGCCTGATGCGACGCTTAACGCGTCTTATCATGCCTACAGGTTTGTGCCGAACCGTAGGCCGGATAAGGCGTTCACGCCGCATCCGGCAGT  >  NC_000913/4614148‑4614394

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