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
A8 F40 I0 R1 23 39.3 1381890 89.2% 1232645 148.7

Breseq alignment

BRESEQ :: Evidence
Predicted mutation
evidence seq id position mutation freq annotation gene description
RA NC_000913_3_hsa_tpiA 2,106,741 A→T 100% S162S (TCT→TCA)  wbbH ← O‑antigen polymerase

Read alignment evidence...
  seq id position ref new freq score (cons/poly) reads annotation genes product
*NC_000913_3_hsa_tpiA2,106,7410AT100.0% 133.0 / ‑6.7 44S162S (TCT→TCA) wbbHO‑antigen polymerase
Reads supporting (aligned to +/- strand):  ref base A (1/0);  new base T (22/21);  total (23/21)
Rejected as polymorphism: E-value score below prediction cutoff.
Rejected as polymorphism: Frequency below/above cutoff threshold.
Rejected as polymorphism: Variant not supported by required number of reads on each strand.

TCTATTAACACCTACGATGAATGCATAAGAGATGATAACCATAAAGACAATTTGCTTACCAGTATTCAGTATAATTGCAAAGATGAATACAATAAAAACAAGTAAAGTAAATGTTTTACTTACCTTTGTATTAGTAAATT‑TTTTAGACCAAATAAATAAAGCAAAAGTAGTTAGAATGATTGGCTGCATGTATGCTGAGAAATTTCTTGATGTGTC‑TTCAACATCAGCATCTCTTATCAAATTCATATAGCTAAGTAAGCTAGTCCCGAACTGGTAGTTACTTAA  >  NC_000913_3_hsa_tpiA/2106597‑2106881
                                                                                                                                                 |                                                                                                                                             
tctcTTAACACCTACGATGAATGCATAAGAGATGATAACCATAAAGACAATTTGCTTACCAGTATTCAGTATAATTGCAAAGATGAATACAATAAAAACAAGGAAAGTAAATGTTTTACTTACCTTTGTATTAGTAAATTGTTTTAGag                                                                                                                                            >  2:311527/1‑148 (MQ=255)
   aTTAACACCTACGATGAATGCATAAGAGATGATAACCATAAAGACAATTTGCTTACCAGTATTCAGTATAATTGCAAAGATGAATACAATAAAAACAAGTAAAGTAAATGTTTTACTTACCTTTGTATTAGTAAATT‑TTTTTGACCaaa                                                                                                                                        <  2:391792/149‑1 (MQ=255)
    ttAACACCTACGATGAATGCATAAGAGATGATAACCATAAAGACAATTTGCTTACCACTATTCAGTATAATTGCAAATATGAATACAATAAAAACAAGTAAATTAAATGTTTTACTTACTTTTGTATTAGTAAATT‑TTTTTGACCaaat                                                                                                                                       >  2:455148/1‑149 (MQ=255)
           aatctaTGAAAACATAAGAGAAGACAACCAAAAAGAATACTTTTTTACCACTATTCAATATAATTAAAAAGATGAATACAATAAAATCAAGTAAAGTAAAGGTTTTACTTACCTTTGTATTAGTAAATT‑TTTTTTACCAAAtaaataaa                                                                                                                                <  2:197727/144‑1 (MQ=255)
                  gAATGCATAAGAGATGATAACCATAAAGACAATTTGCTTACCAGTATTCAGTATAATTGCAAAGATGAATACAATAAAAACAAGTAAAGTAAATGTTTTACTTACCTTTGTATTAGTAAATT‑TTTTTGACCAAATAAATAAAGCAAAag                                                                                                                         <  1:527552/149‑1 (MQ=255)
                    aTGCATAAGAGATGATAACCATAAAGACAATTTGCTTACCAGTATTCAGTATAATTGCAAAGATGAATACAATAAAAACAAGTAAAGTAAATGTTTTACTTACCTTTGTATTAGTAAATT‑TTTTTGACCAAATAAATAAAGCAAAagta                                                                                                                       <  2:491087/149‑1 (MQ=255)
                         tAAGAGATGATAACCATAAAGACAATTTGCTTACCAGTATTCAGTATAATTGCAAAGATGAATACAATAAAAACAAGTAAAGTAAATGTTTTACTTACCTTTGTATTAGTAAATT‑TTTTTGACCAAATAAATAAAGCAAAAGTAGTTAg                                                                                                                  >  2:593619/1‑149 (MQ=255)
                               atgatAACCATAAAGACAATTTGCTTACCAGTATTCAGTATAATTGCAAAGATGAATACAATAAAAACAAGTAAAGTAAATGTTTTACTTACCTTTGTATTAGTAAATT‑TTTTTGACCAAATAAATAAAGCAAAAGTAGTTAGAATGAt                                                                                                            <  1:668184/149‑1 (MQ=255)
                                  atAACCATAAGTACAATTTGCTTACCATTATTCAGTATAAGTGCAAAGATGAATACAATAAAAACAAGTAAAGGAAATGTTTTACTTACCTTTGTATTAGTAAATT‑TTTTTGACCAAATAAATAAAGCAAAAGTAGTTAGAATGATTgg                                                                                                         <  2:581768/149‑1 (MQ=255)
                                  atAACCATAAAGACAATTTGCTTACCAGTATTCAGTATAATTGCAATGATGATTACAATAAAAACAATCAAAGTAAATGTTTTACTTATCTTTGTATTAGTAAATT‑TTTTTGACCAAATCAATATAGCAAAAGTAGTAAGACTGATTgg                                                                                                         >  2:198096/1‑149 (MQ=255)
                                      ccATAAAGACAATTTGCTTACCAGTATTCAGTATAATTGCAAAGATGAATACAATAGAAACAAGTAAAGTAAATGTTTTACTTTCCTTTGTATTAGTAAATT‑TTTTTGACCAAATAAATAAATCAGAATTAGTTAGAATGTTTGTCTga                                                                                                     >  2:618951/1‑148 (MQ=255)
                                       cATAAAGACAATTTGCTTACCAGTATTCAGTATAATTGCAAAGATGAATACAATAAAAACAAGTAAAGTAAATGTTTTACTTACCTTTGTATTAGTAAATT‑TTTTTGACCAAATAAATAAAGCAAAAGTAGTTAGAATGATTGGCTGCa                                                                                                    >  1:339052/1‑149 (MQ=255)
                                         tAAAGACAATTTGCTTACCAGTATTCAGTATAATTGCAAAGATGAATACAATAAAAACAAGTAAAGTAAATGTTTTACTTACCTTTGTATTAGTAAATT‑TTTTTGACCAATTAAATCAACCAAAACTAGTTAGAATGATTGCCTGCATg                                                                                                  >  2:366885/1‑149 (MQ=255)
                                            aGACAATTTGCTTACCAGTATTCAGTATAATTGCAAAGATGAATACAATAAAAACAAGTAAAGTAAATGTTTTACTTACCTTTGTATTAGTAAATT‑TTTTTGACCAAATAAATAAAGCAAAAGTAGTTAGAATGATTGGCTGCATGTAt                                                                                               >  1:457758/1‑149 (MQ=255)
                                             gACAATTTGCTTACCAGTATTCAGTATAATTGCAAAGATGAATACAATAAAAACAAGTAAAGTAAATGTTTTACTTACCTTTGTATTAGTAAATT‑TTTTTGACCAAATAAATAAAGCAAAAGTAGTTAGAATGATTGGCTGCATGTATg                                                                                              >  2:559786/1‑149 (MQ=255)
                                              aCAAATTTCTTAACAGTATTAAGTATAATTGCAAAGATGAATACAATAAAAACAAGTAAAGTAAATGTTATACTTACCTTTGTATTAGTAAATT‑TTTTTGACCAAATAAATAAAGCAAAAGTAGTTAGAATGATTGGCTGCATGTATGc                                                                                             <  2:419947/149‑1 (MQ=255)
                                                 atctGCCTACCAGTATTCAGTATAATTGCAAAGATGAATACAATAAAAACAAGTAAAGTAAATGTTTTACTTACCTTTGTATTAGTAAATT‑TTTTTGACCAAATAAATAAAGCAAAAGTAGTTAGAATGATTGGCTGCATGTATGCTga                                                                                          <  1:216930/146‑1 (MQ=255)
                                                  tttGCTTACCATGATTCTATATAATTGCAAAGATTAATACAATAAAAACAAGTAAAGTAAATGTTTTACTTACCTTTGTATTAGTAAATT‑TTTTTGACCAAATAAATAAAGCAAAAGTAGTTAGAATGATTGGCTGCATGTATGCTgag                                                                                         <  1:40344/149‑1 (MQ=255)
                                                          ccAGTATTCAGTATAATTGCAAAGATGACTACTTTAAAAACAAGTAAAGTAAATGTTTTACTTACCTTTGTATTAGTAAATT‑TTTTTGACCAAATAAATAAAGCAAAAGTAGTTAGAATGATTGGCTGCATGTATGCTGAGAAATTTCt                                                                                 >  2:147375/1‑149 (MQ=255)
                                                           cAGTATTCAGTATAATTGCAAAGATGAATACAATAAAAACAAGTAAAGTAAATGTTTTACTTACCTTTGTATTAGTAAATT‑TTTTTGACCAAATAAATAAAGCAAAAGTAGTTAGAATGATTGGCTGCATGTATGCTGAGAAATTTCtt                                                                                >  1:554767/1‑149 (MQ=255)
                                                           cAGTATTCAGTATAATTGCAAAGATGAATACAATAAAAACAAGTAAAGTAAATGTTTTACTTACCTTTGTATTAGTAAATT‑TTTTTGACCAAATAAATAAAGCAAAAGTAGTTAGAATGATTGGCTGCATGTATGCTGAGAAATTTCtt                                                                                <  1:289053/149‑1 (MQ=255)
                                                              tatgtcatataATAGAAAAGATGAATACAATAAAAACAAGTAAAGTAAATGATTTACTTACCTTTGTATTAGTAAATT‑TTTTTCACCAAATCAATAAAGCAAAAGTATTGAGAATGATTGGCTGCATGTATGCTGAGAAATTTCTTGAt                                                                             <  2:664793/142‑1 (MQ=255)
                                                                   aGTATAATTGCAAAGATGAATACAATAAAAACAAGTAAAGTAAATGTTTTACTTACCTTTGTATTAGTAAATT‑TTTTTGACCAAATAAATAAAGCAAAAGTAGTTAGAATGATTGGCTGCATGTATGCTGAGAAATTTCTTGATGTGTc                                                                        >  1:106820/1‑149 (MQ=255)
                                                                        aaacacAAAAAAGAATACAATAAAAACAAGTAAAGTAAATGTTTTACTTACCTTTGTATTAGTAAATT‑TTTTTGACCAAATAAATAAAGCAAAAGTAGTTAGAATGATTGGCTGCATGTATGCTGAGAAATTTCTTGATGTGTC‑TTCaa                                                                  <  1:237058/144‑1 (MQ=255)
                                                                           tGCAAAGATGAATACAATAAAAACAAGTAAAGTAAATGTTTTACTTACCTTTGTATTAGTAAATT‑TTTTTGACCAAATAAATAAAGCAAAAGTAGTTAGAATGATTGGCTGCATGTATGCTGAGAAATTTCTTGATGTGTC‑TTCAACAt                                                               <  2:373883/149‑1 (MQ=255)
                                                                           tGCAAAGATGAATACAATAAAAACAAGTAAAGTAAATGTTTTACTTACCTTTGTATTAGTAAATT‑TTTTTGACCAAATAAATAAAGCAAAAGTAGTTAGAATGATTGGCTGCATGTATGCTGAGAAATTTCTTGATGGGTC‑TTCAACAt                                                               >  1:139975/1‑149 (MQ=255)
                                                                                aGATGAATACAATAAAAACAAGTAAAGTAAATGTTTTACTTACCTTCAAATAAGTAAATT‑TTATTGACCAAATAAATAAAGCAAAAGTAGTTAGAATGATTGGCTGCATGTATGCTGAGAAATTTCTTGATGTGTC‑TTCAACATCAGCa                                                          >  1:237073/1‑149 (MQ=255)
                                                                                           aTAAAAACAAGTAAAGTAAATGTTTTACTTACCTTTGTATTAGTAAATT‑TTTTTGACCAAATAAATAAAGCAAAAGTAGTTAGAATGATTGGCTGCATGTATGCTGAGAAATTTCTTGATGTGTC‑TTCAACATCATCATCTCTTATCaa                                               >  2:649347/1‑149 (MQ=255)
                                                                                            tAAAAACAAGTAAAGTAAAGGTTTTACTTAGCTTTATATTAGTAACTT‑TGTTTGACCGAATAAAGAAAGCAAAAGTAGTTAGTATGATTGGCTGCATGTATGGTGAGAGATTTCTTGAGGTGTC‑TTCAACATCAGCATCTCTTATCaaa                                              <  2:304196/149‑1 (MQ=255)
                                                                                             aaaacCAATCAAAGTAAATGTTCAACTCACGATTGTATTAGTAAATT‑TTTTTTACCAAATAAATAAATCAAAAGTAGTTAGAATGATTGGCTGCATGTATGCTGAGAAATTTCTT‑ATAACACTTTTTACATCAGCATCTCTTATCAAAt                                             <  2:667958/149‑1 (MQ=255)
                                                                                             aaaaaCAGCGAAAGTAAATGTTTTACTTACCTTTGTATTAGTAAATT‑TTTTTGACCAAATAAATAAAGCAAAAGTAGTTACAATGATTGGCTCCACGTATGCTGAGAAATCTCCTGATCTGCC‑TCCAACATCACCATCTCTTATCAAAt                                             <  2:330460/149‑1 (MQ=255)
                                                                                              aaaaCAAGTAAAGTAAATGTTTTACTTACCTTTGTATTAGTAAATT‑TTTTTGACCAAATAAATAAAGAAAAAGTAGTTAGAATGATTGGCTGCATGTATGCTGAGAAATTTCTTGATGTGTC‑TTCAACATCAGCATCTCTTATCAAAtt                                            >  1:281985/1‑149 (MQ=255)
                                                                                              aaaaCAAGTAAAGTAAATGTTTTACATACCTTTGTATTAGTAAATT‑TTTTTGACCAAATAAATAAAGCAAAAGTAGTTAGAATGATTGGCTGCATGTATGCTGAGAAATTTCTTGATGTGTC‑TTCAACATCAGCATCTCTTATCAAAtt                                            <  1:426494/149‑1 (MQ=255)
                                                                                                 aCAAGTAAAGTAAATGTTTTACTTACCTTTGTATTAGTAAATT‑TTTTTGACCAAATAAATAAAGCAAAAGTAGTTAGAATGATTGGCTGCATGTATGCTGAGAAATTTCTTGATGTGTC‑TTCAACATCAGCATCTCTTATCAAATTCat                                         <  2:690716/149‑1 (MQ=255)
                                                                                                      taaagtaaaTGTTTTACTTACCTTTGTATTAGTAAATT‑TTTTTGACCAAATAAATAAAGCAAAAGTAGTTAGAATGATTGGCTGCATGTATGCTGAGAAATTTCTTGATGTGTC‑TTCAACATCAGCATCTCTTATCAAATTCATATAGc                                    <  1:102137/149‑1 (MQ=255)
                                                                                                       aaagtaaaTGTTTTACTTACCTTTGTATTAGTAAATT‑TTTTTGACCAAATAAATAAATCAAAAGTAGTTAGAATGATTGGCTGCATGTATGCTGAGAAATTTCTTGATGTGTC‑TTCAACATCAGCATCTCTTATCAAATTCATATAGCt                                   <  1:655020/149‑1 (MQ=255)
                                                                                                         agtaaaTGTTTTACTTACCTTTGTATTAGTAAATT‑TTTTTGACCAAATAAATAAAGCAAAAGTAGTTAGAATGATTGGCTGCATGTATGCTTAGAAATTTTTAGTTGTAAC‑GACAAGATCAGCATCTCTTATCAAATTCATATAGCtaa                                 >  1:645367/1‑149 (MQ=255)
                                                                                                             aaTGTTTTACTTACCTTTGTATTAGTAAATT‑TTTTTGACCAAATAAATAAAGCAAAAGTAGTTAGAATGATTGGCTGCATGTATGCTGAGAAATTTCTTGATGTGTC‑TTCAACATCAGCATCTCTTATCAAATTCATATAGCtaagtaa                             >  1:258791/1‑149 (MQ=255)
                                                                                                                       ttacCTTTGTATTAGTAAATT‑TTTTTGACCAAATAAATAAAGCAAAAGTAGTTAGAATGATTGGCTGCATGTATGCTGAGAAATTTCTTGATGTGTC‑TTCAACATCAGCATCTCTTATCAAATTCATATAGCTAAGTAAGCTAGTACCg                   >  1:17427/1‑149 (MQ=255)
                                                                                                                            tttGTATTAGTAAATT‑TTTTTTTTTTATTTTTTAAAGCAAAAATAGTTAGAATGATTGGCTGCATGTATGCTGGGAAATTTCTTGATGTGTC‑TTCAACATCAGCATCTCTTATCAAATTCTTTTATCTATTTAATCTAGTCCAGAACtt              >  2:266597/1‑148 (MQ=255)
                                                                                                                               gTATTAGTAAATT‑TTTTTGACCAAATAAATAAAGCAAAAGTAGTTAGAATGATTGGCTGCATGTATGCTGAGAAATTTCTTGATGTGTC‑TTCAACATCAGCATCTCTTATCAAATTCATATAGCTAAGTAAGCTAGTCCCGAACTgcga           >  2:108129/1‑146 (MQ=255)
                                                                                                                                tATTAGTAAATT‑TTTTTGAACAATTAAGTAAAGCAAAAGGAGATAGAATGATTGGCTGCATGTATGCTGAGAAATTTCTTGATGTGTC‑TTCAACATCAGCATCTCTTATCAAATTCATATATCTAATTAACCTAGTCCCGAACTgttcg          >  2:81812/1‑145 (MQ=255)
                                                                                                                                  ttAGTAAATT‑TTTTTGACCAAATAAATAAAGCAAAAGTAGTTAGAATGATTGGCTGCATGTATGCTGAGAAATTTCTAGATGTGTC‑TTCATCATCAGCATCTCTTATCAAATTCATATACCTAAGAAAGCTAGTCCCGAAACGGTAGtt        >  2:95909/1‑149 (MQ=255)
                                                                                                                                        aaTT‑TTTTTGACCAAATAAATAAAGCAAAAGTAGTTAGAATGATTGGCTGCATGTAAGCTTAGAAATTTCTTGATGTGTC‑TTCAACATCAGCATCTCTTATCAAATTCATATAGCTAAGTAAGCTAGTCCCGAACTGGTAGTTACTTaa  <  2:470739/149‑1 (MQ=255)
                                                                                                                                                 |                                                                                                                                             
TCTATTAACACCTACGATGAATGCATAAGAGATGATAACCATAAAGACAATTTGCTTACCAGTATTCAGTATAATTGCAAAGATGAATACAATAAAAACAAGTAAAGTAAATGTTTTACTTACCTTTGTATTAGTAAATT‑TTTTAGACCAAATAAATAAAGCAAAAGTAGTTAGAATGATTGGCTGCATGTATGCTGAGAAATTTCTTGATGTGTC‑TTCAACATCAGCATCTCTTATCAAATTCATATAGCTAAGTAAGCTAGTCCCGAACTGGTAGTTACTTAA  >  NC_000913_3_hsa_tpiA/2106597‑2106881

Alignment Legend
Aligned base mismatch/match (shaded by quality score): ATCG/ATCG < 3 ≤ ATCG/ATCG < 12 ≤ ATCG/ATCG < 13 ≤ ATCG/ATCG < 27 ≤ ATCG/ATCG < 41 ≤ ATCG/ATCG
Unaligned base: atcg    Masked matching base: atcg    Alignment gap: ‑    Deleted base: ‑

GATK/CNVnator alignment

N/A