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
A12 F1 I1 R1 760 58.2 3022526 90.8% 2744453 102.0

Breseq alignment

BRESEQ :: Evidence
Predicted mutation
evidence seq id position mutation annotation gene description
RA NC_000913 2,911,417 C→T *745* (TAG→TAA)  relA ← (p)ppGpp synthetase I/GTP pyrophosphokinase

Read alignment evidence...
  seq id position ref new freq score (cons/poly) reads annotation genes product
*NC_0009132,911,4170CT96.5% 175.0 / ‑2.8 58*745* (TAG→TAA) relA(p)ppGpp synthetase I/GTP pyrophosphokinase
Reads supporting (aligned to +/- strand):  ref base C (1/1);  new base T (31/25);  total (32/26)
Fisher's exact test for biased strand distribution p-value = 1.00e+00
Kolmogorov-Smirnov test that lower quality scores support variant p-value = 9.99e-01

GCCGGGATCCGCACCGCCGGTGAATTTCCCCAACGCTTTACGCTACTGTGGATCATAACCCTTTCCTCAAACCGCTATCATATGTAGATACAGTATATATCAATCTACATTGTAGATACGAGCAAATTTCGGCCTAACTCCCGTGCAACCGACGCGCGTCGATAACATCCGGCACCTGGTTGAGTTTACCCAGCACGCGCCCCAGCACTTGCAGGTTGTAAATCTCAATGGTCATGTCGATGGTCGCCAGTTGCTGTTTGG  >  NC_000913/2911284‑2911544
                                                                                                                                     |                                                                                                                               
gCCGGGATCCGCACCGCCGGTGAATTTCCCCAACGCTTTACGCTACTGTGGATCATAACCCTTTCCTCAAACCGCTATCATATGTAGATACAGTATATATCAATCTACATTGTAGATACGAGCAAATTTCGGCTTAACt                                                                                                                            >  2:909053/1‑139 (MQ=255)
               gccgGTGAATTTCCCCAACGCTTTACGCTACTGTGTATCATAACCCTTTCCTCAAACCGCTATAATATGTAGATACAGTATATATCAATCTACATTGTAGATACGAGCAAATTTCGGCTTAACTCCCGTGCAACCGAcg                                                                                                             <  1:909053/139‑1 (MQ=255)
                                                          cccTTTCCTCAAACCGCTATCATATGTAGATACAGTATATATCAATCTACATTGTAGATACGAGCAAATTTCGGCTTAACTCCCGTGCAACCGACGCGCGTCGATAACATCCGGCACCTGGTTGAGt                                                                              <  2:750481/127‑1 (MQ=255)
                                                          cccTTTCCTCAAACCGCTATCATATGTAGATACAGTATATATCAATCTACATTGTAGATACGAGCAAATTTCGGCTTAACTCCCGTGCAACCGACGCGCGTCGATAACATCCGGCACCTGGTTGAGt                                                                              >  1:750481/1‑127 (MQ=255)
                                                              ttCCTCAAACCGCTATCATATGTAGATACAGTATATATCAATCTACATTGTAGATACGAGCAAATTTCGGCTTAACTCCCGTGCAACCGACGCGCGTCGATAACATCCGGCACCTGGTTGAGTTTACCCAGCACGCGcc                                                              <  1:379432/139‑1 (MQ=255)
                                                              ttCCTCAAACCGCTATCATATGTAGATACAGTATATATCAATCTACATTGTAGATACGAGCAAATTTCGGCTTAACTCCCGTGCAACCGACGCGCGTCGATAACATCCGGCACCTGGTTGAGTTTACCCAGCACGCGcc                                                              >  2:379432/1‑139 (MQ=255)
                                                               tCCTCAAACCGCTATCATATGTAGATACAGTATATATCAATCTACATTGTAGATACGAGCAAATTTCGGCTTAACTCCCGTGCAACCGACGCGCGTCGATAACATCCGGCa                                                                                         <  2:126494/111‑1 (MQ=255)
                                                               tCCTCAAACCGCTATCATATGTAGATACAGTATATATCAATCTACATTGTAGATACGAGCAAATTTCGGCTTAACTCCCGTGCAACCGACGCGCGTCGATAACATCCGGCa                                                                                         >  1:126494/1‑111 (MQ=255)
                                                                           tATCATATGTAGATACAGTATATATCAATCTACATTGTAGATACGAGCAAATTTCGGCTTAACTCCCGTGCAACCGAcgcgc                                                                                                          <  1:1135082/82‑1 (MQ=255)
                                                                           tATCATATGTAGATACAGTATATATCAATCTACATTGTAGATACGAGCAAATTTCGGCTTAACTCCCGTGCAACCGAcgcgc                                                                                                          >  2:1135082/1‑82 (MQ=255)
                                                                           tATCATATGTAGATACAGTATATATCAATCTACATTGTAGATACGAGCAAATTTCGGCTTAACTCCCGTGCAACCGACGCGCGTCGATAACATCCGGCACCTGGTTGAGTTTACCCAGCACGCGCCCCAGCACTTGCAg                                                 >  2:1188273/1‑139 (MQ=255)
                                                                           tATCATATGTAGATACAGTATATATCAATCTACATTGTAGATACGAGCAAATTTCGGCCTAACTCCCGTGCAACCGACGCGCGTCGATAACATCCGGCACCTGGTTGAGTTTACCCAGCACGCGCCCCAGCACTTGCAg                                                 >  1:1129731/1‑139 (MQ=255)
                                                                                  tGTAGATACAGTATATATCAATCTACATTGTAGATACGAGCAAATTTCGGCTTAACTCCCGTGCAACCGACGCGCGTCGATAACATCCGGCACCTGGTTGAGTTTACCCAGCACGCGCCCCAGCACTTGCAGGTTGTaa                                          <  1:1188273/139‑1 (MQ=255)
                                                                                       aTACAGTATATATCAATCTACATTGTAGATACGAGCAAATTTCGGCTTAACTCCCGTGCAACCGACGCGCGTCGATAACATCCGGCACCTGGTTGAGTTTACCCAGCAcg                                                                  >  2:1050176/1‑110 (MQ=255)
                                                                                       aTACAGTATATATCAATCTACATTGTAGATACGAGCAAATTTCGGCTTAACTCCCGTGCAACCGACGCGCGTCGATAACATCCGGCACCTGGTTGAGTTTACCCAGCAcg                                                                  <  1:1050176/110‑1 (MQ=255)
                                                                                       aTACAGTATATATCAATCTACATTGTAGATACGAGCAAATTTCGGCTTAACTCCCGTGCAACCGACGCGCGTCGATAACATCCGGCACCTGGTTGAGTTTACCCAGCACGCGCCCCAGCACTTGCAGGTTGTa                                           >  1:1177863/1‑133 (MQ=255)
                                                                                       aTACAGTATATATCAATCTACATTGTAGATACGAGCAAATTTCGGCTTAACTCCCGTGCAACCGACGCGCGTCGATAACATCCGGCACCTGGTTGAGTTTACCCAGCACGCGCCCCAGCACTTGCAGGTTGTa                                           <  2:1177863/133‑1 (MQ=255)
                                                                                         aCAGTATATATCAATCTACATTGTAGATACGAGCAAATTTCGGCCTAACTCCCGTGCAACCGACGCGCGTCGATAACATCCGGCACCTGGTTGAGTTTACCCAGCACGCGCCCCAGCACTTGCAGGTTGTAAATCTCaa                                   <  2:1129731/139‑1 (MQ=255)
                                                                                           aGTATATATCAATCTACATTGTAGATACGAGCAAATTTCGGCTTAACTCCCGTGCAACCGACGCGCGTCGATAACATCCGGCACCTGGTTGAGTTTACCCAGCACGCGCCCCAGCACTTGCAGGTTGTAAAt                                        >  2:101723/1‑132 (MQ=255)
                                                                                           aGTATATATCAATCTACATTGTAGATACGAGCAAATTTCGGCTTAACTCCCGTGCAACCGACGCGCGTCGATAACATCCGGCACCTGGTTGAGTTTACCCAGCACGCGCCCCAGCACTTGCAGGTTGTAAAt                                        <  1:101723/132‑1 (MQ=255)
                                                                                             tatataTCAATCTACATTGTAGATACGAGCAAATTTCGGCTTAACTCCCGTGCAACCGACGCGCGTCGATAACATCCGGCACCTGGTTGAGTTTACCCAGCACGCGCCCCAGCACTTGCAGGTTGTAAATCTCAATGGt                               >  2:839154/1‑139 (MQ=255)
                                                                                                  atCAATCTACATTGTAGATACGAGCAAATTTCGGCTTAACTCCCGTGCAACCGACGCGCGTCGATAACATCCGGCACCTGGTTGAGTTTACCCAGCACGCGCCCCAg                                                          >  1:1180342/1‑107 (MQ=255)
                                                                                                  atCAATCTACATTGTAGATACGAGCAAATTTCGGCTTAACTCCCGTGCAACCGACGCGCGTCGATAACATCCGGCACCTGGTTGAGTTTACCCAGCACGCGCCCCAg                                                          <  2:1180342/107‑1 (MQ=255)
                                                                                                     aaTCTACATTGTAGATACGAGCAAATTTCGGCTTAACTCCCGTGCAACCGACGCGCGTCGATAACATCCGGCACCTGGTTGAGTTTACCCAGCAcg                                                                  >  2:413949/1‑96 (MQ=255)
                                                                                                     aaTCTACATTGTAGATACGAGCAAATTTCGGCTTAACTCCCGTGCAACCGACGCGCGTCGATAACATCCGGCACCTGGTTGAGTTTACCCAGCAcg                                                                  <  1:413949/96‑1 (MQ=255)
                                                                                                       tCTACATTGTAGATACGAGCAAATTTCGGCTTAACTc                                                                                                                           <  1:304037/37‑1 (MQ=255)
                                                                                                       tCTACATTGTAGATACGAGCAAATTTCGGCTTAACTc                                                                                                                           >  2:304037/1‑37 (MQ=255)
                                                                                                       tCTACATTGTAGATACGAGCAAATTTCGGCTTAACTCCCGTGCAACCGACGCGCGTCGATAACATCCGGCACCTGGTTGAGTTTACCCAGCACGCGCCCCAGCACTTGCAGGTTGTAAATCTCAATGGTCATGTCGATg                     >  2:1152234/1‑139 (MQ=255)
                                                                                                          aCATTGTAGATACGAGCAAATTTCGGCTTAACTCCCGTGCAACCGACGCGCGTCGATAACATCCGGCACCTGGTTGAGTTTACCCAGCACGCGCCCCAGCACTTGCAGGTTGTAAATCTCAATGGTCATGTCGATGGTc                  <  1:1152234/139‑1 (MQ=255)
                                                                                                            aTTGTAGATACGAGCAAATTTCGGCTTAACTCCTGTGCAACCGACGCGCGTCGATAACATCCGGCACCTGGTTGAGTTTAcc                                                                         <  1:1453626/82‑1 (MQ=255)
                                                                                                            aTTGTAGATACGAGCAAATTTCGGCTTAACTCCTGTGCAACCGACGCGCGTCGATAACATCCGGCACCTGGTTGAGTTTAcc                                                                         >  2:1453626/1‑82 (MQ=255)
                                                                                                                tAGATACGAGCAAATTTCGGCTTAACTCCCGTGCAACCGACGCGCGTCGATAACATCCGGCACCTGGTTGAGTTTACCCAGCAcg                                                                  <  1:1287090/85‑1 (MQ=255)
                                                                                                                tAGATACGAGCAAATTTCGGCTTAACTCCCGTGCAACCGACGCGCGTCGATAACATCCGGCACCTGGTTGAGTTTACCCAGCAcg                                                                  >  2:1287090/1‑85 (MQ=255)
                                                                                                                 aGATACGAGCAAATTTCGGCTTAACTCCCGTGCAACCGACGCGCGTCGATAACATCCGGCACCTGGTTGAGTTTACCCAGCACGCGCCCCAGCACTTGCAGGTTGTAAATCTCAATGGTCATGTCGATGGTCGCCAGtt           >  2:855263/1‑139 (MQ=255)
                                                                                                                     aCGAGCAAATTTCGGCTTAACTCCCGTGCAACCGACGCGCGTCGATAACATCCGGCACCTGGTTGAGTTTACCCAGCACGCGCCCCAGTACTTGCAGGTTGTAAATCTCAATGGTCATGTCGATGGTCGCCAg             <  2:1068717/133‑1 (MQ=255)
                                                                                                                     aCGAGCAAATTTCGGCTTAACTCCCGTGCAACCGACGCGCGTCGATAACATCCGGCACCTGGTTGAGTTTACCCAGCACGCGCCCCAGCACTTGCAGGTTGTa                                           <  2:1029338/103‑1 (MQ=255)
                                                                                                                     aCGAGCAAATTTCGGCTTAACTCCCGTGCAACCGACGCGCGTCGATAACATCCGGCACCTGGTTGAGTTTACCCAGCACGCGCCCCAGCACTTGCAGGTTGTa                                           >  1:1029338/1‑103 (MQ=255)
                                                                                                                     aCGAGCAAATTTCGGCTTAACTCCCGTGCAACCGACGCGCGTCGATAACATCCGGCACCTGGTTGAGTTTACCCAGCACGCGCCCCAGCACTTGCAGGTTGTa                                           >  1:897528/1‑103 (MQ=255)
                                                                                                                     aCGAGCAAATTTCGGCTTAACTCCCGTGCAACCGACGCGCGTCGATAACATCCGGCACCTGGTTGAGTTTACCCAGCACGCGCCCCAGCACTTGCAGGTTGTa                                           <  2:897528/103‑1 (MQ=255)
                                                                                                                     aCGAGCAAATTTCGGCTTAACTCCCGTGCAACCGACGCGCGTCGATAACATCCGGCACCTGGTTGAGTTTACCCAGCACGCGCCCCAGCACTTGCAGGTTGTAAATCTCAATGGTCATGTCGATGGTCGc                <  2:833950/130‑1 (MQ=255)
                                                                                                                     aCGAGCAAATTTCGGCTTAACTCCCGTGCAACCGACGCGCGTCGATAACATCCGGCACCTGGTTGAGTTTACCCAGCACGCGCCCCAGCACTTGCAGGTTGTAAATCTCAATGGTCATGTCGATGGTCGc                >  1:833950/1‑130 (MQ=255)
                                                                                                                     aCGAGCAAATTTCGGCTTAACTCCCGTGCAACCGACGCGCGTCGATAACATCCGGCACCTGGTTGAGTTTACCCAGCACGCGCCCCAGCACTTGCAGGTTGTAAATCTCAATGGTCATGTCGATGGTCGCCAg             >  1:1068717/1‑133 (MQ=255)
                                                                                                                        aGCAAATTTCGGCTTAACTCCCGTGCAACCGAcgcgc                                                                                                          >  1:1163293/1‑37 (MQ=255)
                                                                                                                        aGCAAATTTCGGCTTAACTCCCGTGCAACCGAcgcgc                                                                                                          <  2:1163293/37‑1 (MQ=255)
                                                                                                                        aGCAAATTTCGGCTTAACTCCCGTGCAACCGACGCGCGTCGATAACATCCGGCACCTGGTTGAGTTTACCCAGCACGCGCCCCAg                                                          >  1:866213/1‑85 (MQ=255)
                                                                                                                        aGCAAATTTCGGCTTAACTCCCGTGCAACCGACGCGCGTCGATAACATCCGGCACCTGGTTGAGTTTACCCAGCACGCGCCCCAg                                                          <  2:866213/85‑1 (MQ=255)
                                                                                                                        aGCAAATTTCGGCTTAACTCCCGTGCAACCGACGCGCGTCGATAACATCCGGCACCTGGTTGAGTTTACCCAGCACGCGCCCCAGCACTTGTAGGTTGTAAATCTCAATGGTCATGTCGATGGTCGCCAGTTg          <  2:908926/133‑1 (MQ=255)
                                                                                                                        aGCAAATTTCGGCTTAACTCCCGTGCAACCGACGCGCGTCGATAACATCCGGCACCTGGTTGAGTTTACCCAGCACGCGCCCCAGCACTTGTAGGTTGTAAATCTCAATGGTCATGTCGATGGTCGCCAGTTg          >  1:908926/1‑133 (MQ=255)
                                                                                                                        aGCAAATTTCGGCTTAACTCCCGTGCAACCGACGCGCGTCGATAACATCCGGCACCTGGTTGAGTTTACCCAGCACGCGCCCCAGCACTTGCAGGTTGTAAATCTCaa                                   <  2:225952/108‑1 (MQ=255)
                                                                                                                        aGCAAATTTCGGCTTAACTCCCGTGCAACCGACGCGCGTCGATAACATCCGGCACCTGGTTGAGTTTACCCAGCACGCGCCCCAGCACTTGCAGGTTGTAAATCTCaa                                   >  1:225952/1‑108 (MQ=255)
                                                                                                                        aGCAAATTTCGGCTTAACTCCCGTGCAACCGACGCGCGTCGATAACATCCGGCACCTGGTTGAGTTTACCCAGCACGCGCCCCAGCACTTGCAGGTTGTAAATCTCAATGGTCATGTCGATGGTCGCCAGTTGCTGttt    >  1:792241/1‑139 (MQ=255)
                                                                                                                        aGCAAATTTCGGCTTAACTCCCGTGCAACCGACGCGCGTCGATAACATCCGGCACCTGGTTGAGTTTACCCAGCACGCGCCCCAGCACTTGCAGGTTGTAAATCTCAATGGTCATGTCGATGGTCGCCAGTTGCTGttt    >  1:1014835/1‑139 (MQ=255)
                                                                                                                        aGCAAATTTCGGCTTAACTCCCGTGCAACCGACGCGCGTCGATAACATCCGGCACCTGGTTGAGTTTACCCAGCACGCGCCCCAGCACTTGCAGG‑TGTAAATCTCAATGGTCATGTCGATGGGCGCCAGTTGCTGTTTg   >  1:284369/1‑139 (MQ=255)
                                                                                                                          cAAATTTCGGCTTAACTCCCGTGCAACCGACGCGCGTCGAt                                                                                                    >  1:123925/1‑41 (MQ=255)
                                                                                                                          cAAATTTCGGCTTAACTCCCGTGCAACCGACGCGCGTCGAt                                                                                                    <  2:379278/41‑1 (MQ=255)
                                                                                                                          cAAATTTCGGCTTAACTCCCGTGCAACCGACGCGCGTCGAt                                                                                                    >  1:379278/1‑41 (MQ=255)
                                                                                                                          cAAATTTCGGCTTAACTCCCGTGCAACCGACGCGCGTCGAt                                                                                                    <  2:123925/41‑1 (MQ=255)
                                                                                                                          cAAATTTCGGCTTAACTCCCGTGCAACCGACGCGCGTCGATAACATCCGGCACCTGGTTGAGTTTACCCAGCACGCGCCCCAGCACTTGCAGGTTGTAAATCTCAATGGTCATGTCGATGGTCGCCAGTTGCTGTTTgg  >  2:1094738/1‑139 (MQ=255)
                                                                                                                                     |                                                                                                                               
GCCGGGATCCGCACCGCCGGTGAATTTCCCCAACGCTTTACGCTACTGTGGATCATAACCCTTTCCTCAAACCGCTATCATATGTAGATACAGTATATATCAATCTACATTGTAGATACGAGCAAATTTCGGCCTAACTCCCGTGCAACCGACGCGCGTCGATAACATCCGGCACCTGGTTGAGTTTACCCAGCACGCGCCCCAGCACTTGCAGGTTGTAAATCTCAATGGTCATGTCGATGGTCGCCAGTTGCTGTTTGG  >  NC_000913/2911284‑2911544

Alignment Legend
Aligned base mismatch/match (shaded by quality score): ATCG/ATCG < 3 ≤ ATCG/ATCG < 30 ≤ ATCG/ATCG < 36 ≤ ATCG/ATCG < 39 ≤ ATCG/ATCG < 40 ≤ ATCG/ATCG
Unaligned base: atcg    Masked matching base: atcg    Alignment gap: ‑    Deleted base: ‑

GATK/CNVnator alignment

N/A